Meruem of Hunter × Hunter is a genocidal monster. He killed his own mother right out of the womb, by tearing his way out and from than on made plans and took actions that caused the deaths of hundreds of thousands, all well taking a sadistic pleasure from it on his drive to absolute power. But his death, going off to find Komugi as he slowly dies from a deadly toxin, all to play a few last games of Gungi with her and eventually dying in her arms, is one of the series biggest Tear Jerkers.
Vegeta's death after Frieza gives him a No-Holds-Barred Beatdown. Vegeta has been despicable for sixty-something episodes, and has just killed a village full of cute alien children and their big brothers. You'd expect a character of this type to die in a spectacular explosion, then never be seen again. But instead, we get a lengthy Final Speech about his genuinely horrendous childhood, and see Vegeta crying as he begs Goku to kill Frieza and avenge their people. Then Frieza gets impatient and shoots him. (Like almost everyone in the series, he gets better.)
Subverted with Frieza's death. A few minutes before his death, he is split in two parts by a reverse attack. He is dying and asks Goku for mercy. Although Goku was aware of all of the horrible things Frieza did, he still manages to show some sympathy and gives Frieza some of his energy. However, Frieza immediately used it to try to kill Goku (again), which fails.
Witchblade with Maria, a cloneblade. After failing to get the Witchblade from Masane, she is stabbed by her. While dying, she sees a ghost/hallucination of her biological mother Reina Soho, and asks her "mother" to tell her that she loves her.
Gunnm had Zapan, a bounty hunter cyborg whose problems can all be ultimately traced back to Alita. Exposition time: Alita beat him up and humiliated him for not wanting to serve as cannon fodder for her quest against a brain-eating cyborg. From there, he tries to stop her from helping a wanted fugitive escape, at which point, Alita dupes the security bots on site into thinking that Zapan was trying to steal her proof of bounty. She rips his face off and leaves him for dead, only to be discovered with partial memory loss by a young woman named Sarah who worked at a soup kitchen. The two fall in love, and live fairly happily until Zapan sees Alita on television, gets horrific flashbacks, and has a mental breakdown, screaming "This isn't my face!" as he tears off most of the skin on his face. As he thrashed in pain, he killed several winos, and, more importantly, accidentally decapitated Sarah. He became wanted and horrifically depressed. Alita hunts him down, then, after mind-raping him a second time, she lets him get devoured by cyborg dogs. Almost done: after he's resurrected and put in the super-robot-killing-machine Berserker Body, he starts wreaking havoc on Scrapyard, finally being hit by several 'Collapser' bullets from Alita, and the two are plummeting from several miles in the air, both horrifically wounded and on the verge of death. But suddenly, Zapan wakes up: he's lying on a sleeping mat in the market next to Sarah, who comforts him after he briefly recounts his horrible nightmare. She hugs him and tells him that he's not a monster like the Zapan in the dream is, and that she'll always be with him...and then he snaps out of his mortal-wounding induced hallucination, right back to where he was. He screams Sarah's name once, then continues to disintegrate, but not before flapping his wings just once, enough to break Alita's fall and save her.
The sad fate of a sentient Artifact of Doom in Magical Girl Lyrical Nanoha A's, who requested that she be sealed before she caused any more destruction. "Right now, I'm the happiest magical tome in the whole wide world." She gets a semi-reincarnation in Reinforce Zwei who was created by Reinforce Eins' (said Anti-Villain tome) and Hayate's linker cores. Zwei has a completely different personality, and Hayate and Signum continue to refer to Eins watching them from heaven.
The MOVIE 1st gives Precia Testarossa an absolutely heartbreaking death scene. As she falls into an endless abyss, she remembers that Alicia wanted a sister, and realizes that she should have treated Fate as another daughter, and not as a Replacement Goldfish for Alicia, but by then, it's too late for her to make amends or even apologize.
Sure, there's almost always a monster amongst the current villains of the week (Often, the doctor controlling them and the Magnificent Bastard, Kane, in the Psychic Assassins), but at the same time, you got the Greek Gods who, other than Artemis, were genuinely unaware of what happened to them before, and many of 'em died in a very horrible way. Atlas and Pan even walked right in to a burning island knowing they wouldn't be able to save Artemis. Minotaur and Poseidon willingly catch fire and die (Achilles wasn't that likable anyways).
In the Psychic Assassins arc, Kane is a Magnificent Bastard, but Lena and her little brother Phil's Heroic Sacrifice more than makes anyone sad. Despite how Mai is shown to be rather cold, she makes a Heel-Face Turn but then fades out of existence because the timeline changed and made it so that she didn't exist.
Joe's friends from the orphanage became villains of the day, but they all had bombs inside of them. Because they didn't want to kill Joe, they quickly huddled together, said "Bye!" to him, and exploded. The house they lived in caught fire and burned down.
The other 00 cyborgs!
0011. He just wants to go back to his family, but after losing to the cyborgs once, his mind gets controlled by Black Ghost, and he dies as a brainwashed machine.
0012. Sure, love did make that odd cyborg crazy, but as the mansion burned down, 004, 007, and 009 spotted her in the window with her husband who never returned to her, who she waited for all these years.
0013...granted he wasn't that much of a villain, but he couldn't take it anymore and jumped off a cliff to his death since he knew he would never escape from Black Ghost, and 009 stayed by his side as he died of his injuries.
0010+ and 0010- were...rather unlikable, and had almost no redeeming qualities. Until you realize that something wasn't exactly explained and that they possibly made two identical twins into cyborgs who couldn't touch each other...and when the last we see of 0010 is both of them lying on the ground grabbing each other...
The 1968 series has one in the second episode. Cyborg X was made to destroy the cyborgs (specifically, 009) by one of Gilmore's ultra rivals. It's actually revealed that he was someone named Naku, and had a girlfriend he left behind, apparently having "died" in a car accident. She was actually willing to kill Cyborg 009 if it meant saving Naku's life, but then she realized that they are both still humans, despite how Naku is under control by the evil Doctor of the week. Naku, at first, was just carrying out orders to destroy 009, but eventually comes to hate him...so he tried to kill him with an automatic rifle...but his girlfriend pushed 009 out of the way and was killed. Naku released the hostages (003 and 007) and took a cobalt bomb. He said "bye" to everyone and then flied towards Omega, the mad scientist's island. Omega then screamed, "NO WHAT ARE YOU DOING?!" as Cyborg X crashed right into the island...detonating the bomb. Some of the saddest music play, and it's actually quite intense for something made in 1968.
Many villains from Fist of the North Star are given this treatment. One of the earliest examples is with Shin, a rival of Kenshiro and the leader of the city of Southern Cross. Everything he had done, from beating and scarring Kenshiro to becoming a tyrant, was all for the affections of Yuria, Kenshiro's lover, who, unfortunately, did not requite his affections. After being defeated by Kenshiro and explaining what happened with him and Yuria, he opts to end his own life and throws himself off a tower, rather than allow Kenshiro's Hokuto Shinken techniques to claim his life. Afterwards, Kenshiro gave him a proper burial, out of respect for his rival.
Ray Beams dies like this, reaching for the wedding ring on her severed arm across the room.
Even the resident Big Bad Dewey gets this toward the end, with Holland expressing pity for his brother after the latter's suicide.
Miyu's reaction to Alyssa's death at the end of the Searrs arc of Mai Hime: "Her beautiful golden light is gone!", followed by an anguished cry of "Why did this have to happen to her?!" and a burial at sea, of sorts.
Gluttony is swallowed by Pride so the latter can gain Gluttony's ability to sniff out his enemies. Gluttony goes out crying and screaming, begging Lust to save him (despite her already being dead), so it's hard not to feel sorry for him.
Envy, despite being the worst monster amongst the homunculi, manages to evoke feelings of pity before his death. The jealousy that was used to create him ensures he could only ever despise humans, whom he could emulate but never truly be like.
A non-Homunculi example occurs in the case of the Slicer Brothers. Despite being Serial Killers, they clearly had some sense of honor and were willing to answer Ed's questions about the Fifth Laboratory once Ed defeated them and treated them with human decency. The older brother gets killed by Lust suddenly just as he's about to spill some secrets which causes the younger brother to utterly freak out. Envy then decides to Kick the Dog by mocking the younger brother and repeatedly stabbing his blood seal until he's dead.
In the first anime, most of the homunculi go out like this as well:
Lust's death is especially moving, as she has practically switched sides at this point and is about to be finished off by Wrath while she ponders her existence one last time.
Gluttony's death in The Movie could almost be considered a Mercy Kill. He loses his purpose for living after Lust's death, and only continues to be a villain because Dante turned him into a mindless killing machine.
Greed tells Ed the secret to killing the homunculi before dying by his hand, and says that he is counting on him.
A non-homunculus example would be Scar, despite him being more of an anti-villain: he saves Al's life by turning him into the Philosopher's Stone at the cost of his own life. It is very sad, considering that he wanted a genuine relationship with his brother, as revealed in his speech to Lust.
The series' version of Shou Tucker is a rather bizarre and controversial example. He doesn't really die, and the things he's done make you wish he did. By the end though, not feeling a shred of pity for the guy is almost impossible. Especially when you consider he really wanted to atone for his crimes and bring back his daughter, but only ended up committing more and losing what was left of his mind.
Nearly any major death in Naruto. Kishimoto loves emotional death scenes with flashbacks, thus villains and good guys get equal treatment, even when they don't have a case of Redemption Equals Death.
Kimimaro and Sasori. And Danzo. And Kisame.
Orochimaru got a much more effective send-off in the anime, where viewers were treated to Orochimaru's idealistic beginning and slow and inexorable descent into evil.
One Piece has all shades of villains; one end has those who could take enough damage to kill someone in the real world ten times over, and still have fans say that they deserve worse. The other end has some more sympathetic villains, such as...
Mohmoo the sea cow, from the Arlong arc. He's renowned as a vicious monster capable of destroying an entire town, but on-camera, he's basically a Butt Monkey to the Straw Hats…and most of the time, he's seen crying because of it.
After a Villainous Breakdown and, consequently, a failed Motive Rant, Light gets one of the most touching sendoffs ever. In the anime, anyway. In the manga, he begs for his life like the little worm he is. The manga's epilogue chapter ends with a large procession, holding a candle-lit vigil for their dead "savior".
Several of the villains from the anime version of Sailor Moon.
Second season: The only one to have a sympathetic death without also going through Redemption Equals Death is Esmeraude, who got turned into a gigantic dragon by Wiseman and is killed unwittingly by the Sailor Senshi. She cries out to Prince Diamande before passing away in her human form.
Third season: Kaolinite. All she wanted was to be with Professor Tomoe. Then Mistress 9 killed her upon her resurrrection.
Also, Viluy was a bit of an Alpha Bitch, but her death was so utterly cruel that one has to have pity for her.
Fifth season: All of the Sailor Animamates in some form as most are killed for failing their ruler in some way. They are all given sympathetic deaths in the process, either fearful for their lives, calling out to loved ones, or in Tin Nyanko's case, still half-possessed by Galaxia and incapable of taking action. The viewer learns after this one that all of the Animamates used to be legitimate, good Sailor Senshi who were turned by Galaxia, making their words upon dying even more sympathetic upon reflection.
Nakago in Fushigi Yuugi. Throughout the whole series, he does any number of horrible things that make you want him to just get killed already. But as he is bleeding to death, out comes the angsty childhood flashback. Turns out, he was an incredibly cute kid who the creepy emperor decided to use as a personal sex slave. This was after he killed his own mother by accident. And by the way? That happened while his mother was being gang raped. Trauma and cute little kid tears galore.
Barasuishou gets one in the finale of the second season, breaking apart in her creator's arms and begging him for help while Jun looks on in horror.
Hansel and Gretel from Black Lagoon. Throughout most of the arc, they're depicted as being malicious, cruel, smiling psychopaths. Only it turns out that they were forced to act in horrifying child porn, where they were not only raped repeatedly but also forced to kill other children. Needless to say, it's easy to see why they were so fucked up, and it's easy to at least feel sorry for them. Then, after Balalaika gives Hansel a Shut Up, Hannibal! treatment as punishment for harming the subordinates she's so protective of, she orders her men to blow his hand and leg off. When he's lying there, crying and bleeding to death, it's easy to forget that he was a mass murderer. This is taken to further extremes with his sister Gretel, who states that she always wanted to see the ocean and has a heartbreaking Evil Cannot Comprehend GoodDoes Not Know How To Say Thanks moment when Rock offers her kindness and sheds tears for her. When they finally reach a seaport and her wish is granted, her brains get blown out by an assassin hired by Hotel Moscow since karma has caught up with her, and she dies saying that the sky and the sea is beautiful.
The Anti-Spirals of Tengen Toppa Gurren Lagann spend much of the show's second half brainwashing (and, in The Movie, raping) the hero's girlfriend, programming the moon to crash into the earth, killing most of the hero's companions, and generally trying to inspire as much despair as possible. Their last words? "Make sure...to protect the universe." This, combined with the fact that during the final battle they revealed how much they sacrificed to do so, almost puts them in Anti-Villain territory.
The Legend of Zelda: Four Swords Plus manga: near the end, Shadow Link is (apparently) dying, and the last words he says shows you that he never wanted to be the bad guy, he just wanted someone he could call a friend.
Ulquiorra Cifer, dying right before finally realising what it means to be a human being. His last scene, where he turns and reaches out to his former captive Orihime, is very sad and very touching.
Ulquiorra: Do I...scare you, girl? Orihime: No, you don't.
Nnoitra Gilga has a rather different flavor to his Alas Poor Villain than Tia and Stark. With Tia and Stark, the tragedy is that they were both good people who were dragged into this war out of a desire to protect their friends, no different from any of the heroes fighting, and their deaths even though Tia (barely) lived were a pointless waste orchestrated by a man who couldn't give less of a shit about them. The empathy comes from the defiant but also somewhat pathetic way Nnoitra faced his end: Nnoitra simply hurls himself at Kenpachi to satisfy his psychotic death wish because he can't stand the idea of living because of another person's mercy.
Wonderweiss Margela. Captain-Commander Yamamoto, always cold and stern, expresses pity for the kid when he kills him.
Yamamoto: Poor thing... Were your emotions taken away from you too? [Stares at Aizen] That was cruel of you.
Even Yammy of all people, gets a certain amount of pathos in the end, as his dog Kokapurro comes and sits next to him and howls. Side materials make this worse, showing that while Yammy was absolutely a stupid, uncaring thug, his simple presence kept Kokapurro alive in the Crapsack World that is Hueco Mundo, and that while he kicked it around, he never chased it away.
Gin Ichimaru. Goes out a la Tousen, although he actually gets to see Rangiku right before he dies.
In the X-Cution arc, we have Jackie Tristan. Not only did she have the best Freudian Excuse of the Fullbringers, but in her mix of Better to Die Than Be Killed and Heroic Sacrifice, she tells Renji that she wishes he would've saved her when she needed it. And then it's subverted: she lived to tell in the end.
Charlotte Cuulhorne, a member of Barragan's Fracción, is a massive Fighting Narcissist and Large Ham. However, when he's defeated and fatally injured by Yumichika Ayasegawa, Charlotte accepts his death quietly and just tells his rival "You're such a piece of work..." as he fades away. It's surprisingly effective.
Shockingly, Aizen got one from Ichigo after his defeat. Ichigo muses that what drove him wasn't at first a lust for power or evil, but simply the soul-crushing loneliness of being without a rival or peer.
In the Thousand Years Old Blood War, we have Royd Lloyd. Just... Royd Lloyd. Not only he was subjected to a massive Curb-Stomp Battle from Yamamoto while posing as his leader Juhabach, but before Juha goes "You Have Outlived Your Usefulness", he looks so damn happy as he lays dying. And the first page of 510 shows his backstory as well...
Before that, Ayon, of all characters, gets this, absorbed by Vandenreich member Quilge Opie.
Chrono Crusade gives a large number of the villains this sort of send-off, particularly in the manga version. Rizelle's dying words are asking Aion if she was "any use to you", Genai and Viede die fighting side-by-side with Genai's last words implying that he's going to be by Rizelle's side, Fiore dies (or is frozen in crystal, depending on the version) while trying to protect Joshua, and Aion has a heart-to-heart chat with Chrono about his motivations—which includes finding out the truth about theirmother—before they engage in their final battle.
Izumi in Gantz is an Ax-CrazyBlood Knight who goes on a shooting spree just to be killed and allowed to return to the game. Then, he gets an absolutely awesome death scene where he singlehandedly slaughters twenty-odd vampires sent to kill him and has a touching moment where, in his dying breath, he more or less apologizes to his girlfriend for not paying her the attention she deserves and promises to take her on a date.
Nishi's horrible death in the anime. He goes on a lengthy speech of how much he loves and misses his mother before his death.
Copy Rezo from the end of Slayers season one. As well as Eris a few episodes earlier. (Both had somewhat less sad deaths in the original novels, though still pitiable.)
Harry MacDoogal from Outlaw Star. Yes, he's a villain, and an Ax-CrazyStalker with a Crush at that, but when Hazanko destroys him, Melfina cries out for him, and when he appears as a mechanical "phantom" before Gene and Khan and helps to open the door, he has some poignant final moments.
Also with Hanmyo. Jim didn't even realize that the assassin that was out to take out their lives is in that spaceship he destroyed.
In Code Geass Nightmare of Nunnally, Rolo gets one as his body rots away in Anya's arms. After realizing that she was watching over him all the time, he asks whether he, as a Wired, could return to C's world, and she says that she doesn't know. Charles and Marianne manage to accept their deaths relatively calmly compared to the original anime, and Nunnally is clearly saddened by their passing.
Lelouch's death, one of the saddest scenes in the series.
Mikoto from Flame of Recca is considered 'the female Mokuren': smug, bitchy, and monstrous. But then, they both get into a relationship, and while still smug and a monster, Mikoto somewhat mellows a bit. Then, Mokuren conveniently kills her to give him an advantage while she's begging him to stop fighting altogether. Sure, she's done lots of horrible things, but God, she looked so pitiful during her death that the one you wanted to die is not her, but Mokuren.
The circus performers of Black Butler. In the chapters after they are slaughtered en masse, they are still shown to be sympathetic characters feeling indebted to a monster for saving them from life as cripples in a slum, and trying to the save other children at a workhouse. This goes up majorly when it turns out that there were no other children and all of them died for nothing.
Madame Red's death was a real Tear Jerker, especially after hearing her backstory.
In the anime version, the puppet man who turned Lizzy into a puppet/doll makes a short speech about how he's been having a feeling that he's not human at all...
Also in the anime, AloisTrancy from the second season gets his skull crushed between the hands of his faithful servant. Immediately after making a speech about how said servant is the most important person in his whole world. While messily sobbing.
Ophelia started gleefully Ax-Crazy, got worse, but faced death with dignity and gratitude.
Isley, the Awakened Being responsible for the carnage the Claymores suffered during the Northern Campaign, spent his final moments wishing for just a little more time with Priscilla and Raki, whom he had come to see as his family. It helps that his death is positively horrendous, having spent years running away from a pack of soulless, nigh-indestructible demons and finally being devoured alive by them, bite by bite.
Riful of the West frequently treated her lover Dauf like dirt. Yet even after she had lost one arm and one leg and felt the obscenely powerful Priscilla approaching to kill her, she was still unwilling to abandon him (having lost both his legs and one arm) in order to save her own life. Priscilla then proceeded to ram an arm through her and shoot innumerable spikes through her from within.
Oh, Christ, and Duph. After he threatens the nigh-godlike Priscilla with evisceration should she harm Riful, Priscilla proceeds to tear out his guts, then murders Riful and leaves Duph to die. What does Duph do? He lets himself get hit by the parasites o' doom that have been shot all over the countryside, turning him into a skull-faced berserking monster that pounds Priscilla into the ground, all while holding Riful's body in one fist. Eventually, he is killed, but not before it's clear how far he was willing to go to avenge the only person he cared about.
Kaori Yuki seems to enjoy doing this with her Big Bads.
The Man Behind the Man of Zambot 3 is this incarnate - a sentient computer core whose entire purpose is to purge evil from the universe. As it dies, it explains that everything it did was in the name of wiping out evil, including humanity, and demands to know why Kappei protected humanity. Upon hearing Kappei's reply, it deems Kappei to be good, and asks him one last, depressing question, "Will the evil-minded people of Earth... ever thank you? Will that planet Earth... ever have that sort of kindness? " before answering its own question, "You are the victor! However... there cannot be any good people on your Earth who are going to thank you!! In this evil-filled Earth... will there even be... one single lifeform... who will appreciate what you did...?" before dying.
Cowboy Bebop's twentieth episode featured a mad assassin of Joker likeness named Tongpu, aka Mad Pierrot, who, in the climax, lured Spike into an amusement park to kill him. It's revealed that he was an old man with the mind of a child from inhumane experiments, and when Spike stabbed him in the knee, Pierrot rolled into a ball and cried for his mommy. He then died from having a robotic amusement park animal's foot crush him.
This is something of a recurring theme in Cowboy Bebop - any time they successfully track down and kill a mark, it turns out they had a reason for doing what they did.
In The Movie, the Big Bad Vincent Volaju was originally lovers for Electra, and that Electra was forced to deliver a mercy kill to Vincent at the end.
The guy who steals a spider-tank as a replacement for his own body which is dying of a progressive degenerative disease, because he wants to visit his mother one last time.
The villain from the game, who became a terrorist to protect her dead lover's utopian ideas from commercial exploitation.
In the Gungrave anime, this happens to nearly all villains. It would be easier to list who doesn't cause this reaction from the audience. It helps that, despite committing many cruel deeds, most of them are anti villains who have sympathetic motives behind their actions.
El Cazador de la Bruja has one for Ellis' creepy and occasionally outright psychotic stalker L.A.. It begins when Rosenburg, who he outright hates at this point and tries to kill when he meets him, tells him that all the feelings he had for Ellis were fabricated by him, just before brainwashing him into forgetting about Ellis and reverting to cold, ruthless assassin mode, and sending him off to kill Ricardo. One fight scene between them later, he starts to remember Ellis, going into a full-on Villainous Breakdown when Ricardo refuses to let him cut out and meet up with her again. In the end, he gets fatally shot, and starts hallucinating Ellis as the little girl standing over him (who's actually Lirio), realizing, as he dies, that he loved her even before Rosenburg brainwashed him into doing it.
In Kekkaishi, the Big Bad, Byakku, is mostly shown as being a completely cold, heartless monster, who sacrifices his own soldiers with mathematical precision, turns people into puppets, and kills anyone who stops being useful to him. The Woman Behind The Man, Hime, we don't see much of, but she at least manages to come across as callous, seemingly sending her armies against the Kekkaishi's Protectorate on a selfish whim. In their interactions with each other, Hime is a Spoiled Brat drama queen, and Byakku is as icy as ever. At the end, however, their entire dimension is collapsing, and as the heroes make their escape, Byakku - previously killed by an old enemy - gets better, and, rather than flee, rushes to the side of his rapidly-weakening princess. With stoic calmness, he fulfills her final wishes (even though she wonders why he isn't saving himself), as the fortress-like dimension briefly returns to its original appearance - an endless, golden wheat-field. They share a tender moment, reflecting on what's really important, before the dimension collapses around them, reducing them both to nothingness.
Hellsing gives us Rip Van Winkle, an evil Nazi vampire and huntress. She starts panicking when Alucard gets within fifteen miles of the ship she's on. After that she's curled up in a ball crying. When Alucard shows up, she spends most of the fight in abject terror, and stops crying only long enough to shoot Alucard. That works about as well as could be expected, and he slowly impales her with her own musket, giving the viewer about three minutes of rape imagery while he slowly drinks the blood that has spilled out onto the deck, using ten extra arms growing from his back to hold her still and grope her. Then he finally puts her out of her misery...by biting into her neck with his mouth full of sharp teeth and sucking her dry, followed by him absorbing her. Her commander watches her over a satellite video link, congratulates her, and opts to give her a "hunter's death" instead of flipping the remote kill switch. This scene is often cited when discussing whether Alucard is an Anti-Hero or a Villain Protagonist.
Also notable is that she's the only Millennium agent that doesn't boast how they're going to kill Alucard. Rip knows how dangerous Alucard is and does her best to get away, but Alucard hunts her down.
Kuruku from Unico in the Island of Magic fits this trope quite well, given both his backstory and the "kill'em with kindness" death he suffers.
Even though he was an unrepentant murderous rapist, Shira's death in Blade of the Immortal was so gruesome and horrifying that any hint of satisfaction the audience may have felt promptly evaporated. That he uses his dying breath to tell Renzo not to follow in his footsteps probably had something to do with it as well. There is a distinct possibility that he was merely messing with him, but still...
Heartcatch Pretty Cure gives us Dark Pretty Cure. She spends most of the series as a stoic Evil Counterpart who seems to exist only to dog Yuri and provide a strong opponent for the Cures once in a while. Then episode 47 reveals that she just wants to cement her place as Sabaaku's real daughter, having been made to replace Yuri. Then episode 48 gives us her death scene proper, where Sabaaku comforts his now-badly-injured "other daughter" and refers to her as Yuri's sister. The vulnerability coming from the heretofore borderline-emotionless Dark as she is embraced by Sabaaku and fades away makes it even more saddening.
Blue Submarine No. 6 has Dr. Zorndyke. who explains that after losing his wife and child, the world seemed wrong, and he set about changing it, before ripping out his own heart. And Verg too, if he did die at the end.
Suitengu Choji seems like a power hungry, money obsessed Magnificent Bastard in Speed Grapher, but near the end of the series, his backstory is revealed, turning him into a more sympathetic villain. Everything he had done in the anime was for revenge, against the people who had destroyed him and against the society that had allowed it. Just before the end, he spares his blind and helpless enemy, and then spends his last moments with his most faithful servant.
Said faithful servant (Tsujido), too. He was tortured, disfigured and likely violated alongside other persons in a Tokyo club for the rich and depraved; he was rescued by Suitengu, recovering a part of his self-worth in the process. While he is NOT a saint, the big reason why he works for Suitengu is that he wants to thank him for saving his life in all senses (and he might be in love with him as well), therefore staying with his boss as they both die. Not to mention, another of his Punch Clock Villain companions (himself also a torture victim rescued by Suitengu) also dies.
The Nothing Card in the second movie of Cardcaptor Sakura, a Woobie, Destroyer of Worlds and Dark Magical Girl. She had a sympathetic backstory, imprisoned alone beneath Clow Reed's house to act as a sponge for the negative energy the Clow Cards created. She escaped when Clow Reed's house was demolished and systematically stole the cards from Sakura Kinomoto as well as erasing parts of her hometown. Sakura managed to convince the Nothing to perform a Heel-Face Turn.
In Mirai Nikki, virtually of the Future Diary owners receive this trope although Yukiteru Amano and Kamado Ueshita may be excused and others have taken their own Heel-Face Turn. Most notably are Yuno Gasai who suffered a terrible childhood, went insane and became a god in order to repeat time to respend her days with her loved one Yuki, until she eventually is Driven to Suicide to ensure he becomes a god. She gets better though.
Then we have Tsubaki Kasugano, the local Woobie, Destroyer of Worlds who went mad after years of orphanhood and sex slavery. The manga had her angrily and despairingly scream as her Tragic Keepsake is used in her death, but the anime makes her look more sad than angry...
This is rare and far between in a work such as Berserk where every villain who has been presented and killed off deserved what was coming to them. Except one: Rosine. Poor Rosine grew up in an abusive household and used the myths about the elves in a nearby valley as her only refuge. One day she couldn't take the abuse any longer and decided to run away to the valley in order to make her dreams come true, but unfortunately, she would learn that there were no such things as elves, making her reach her breaking point which in turn allowed her to sacrifice her parents so that she may become her vision of an elf. She intended to make a paradise with the minions that she created, but it was anything but. Then Guts, who at this point in the manga is in hardcore post-Eclipse vengeance mode and doesn't care about any of this, comes and brutally and relentlessly hunts Rosine and eventually mortally wounds her. As she lay dying, it was revealed to her that there were such things as elves, but she just wasn't one of them, making her regret sacrificing her parents and then tries to return home to them, but dies mid-flight. It's made even sadder in that both she and her parents are in no blissful afterlife, but in Hell because of the way sacrifices to become demons work in Berserk.
The Count was a murderous man-eating tyrant. But he wasn't always that way. He used to be a loving husband and father who was devoted to his duty of hunting heretics. Then he found his wife engaged in an orgy with fellow demon worshipers. He nearly committed suicide in despair, but his blood activated a Behelit, and he sacrificed his wife to become a demon. Even as a demon, he still loved his daughter Theresia, and ultimately refused to sacrifice her to save himself from dying despite knowing he would be Dragged Off to Hell. The scene with Theresia desperately trying to save her father's soul from being sucked into Hell is both horrifying and sad.
Z-one in Yu-Gi-Oh! 5Ds. After his defeat at the hands of Yusei, he feels remorse for what he has done and asks Yusei if what he did was wrong. Yusei tells him that all he wanted to do was save his future, and plans to sacrifice himself to save Neo Domino City from being crushed by the Ark Cradle. However, Z-one tells Yusei that the future is entrusted to him, and he crashes into the Ener-D reactor, sacrificing himself in Yusei's place. Before dying, he tells his dead friends Antinomy, Aporia and Paradox that he'll be joining them, before he finally dies.
Zeta Gundam: The deaths of antivillains Mouar Pharaoh, Four Murasame, and Rosamia Badam are all very sad. Perhaps the most classic example, however, is the death of The Rival, Jerid Messa, a surprisingly sympathetic Jerkass Woobie, whose exit is depressing, not only because he is dying, but because of how utterly pointless it is..
Haman Khan's suicide in Mobile Suit Gundam ZZ, after Judau makes her realise that she is in fact the villain of the peace. The death of Glemmy Toto, child-abusing teenage dictator that he may have been, can also provoke this reaction, given that he dies at the hands of the one person he cared about.
In Narutaru, there is Aki Honda's death. Extremely cruel and nasty Alpha Bitch without any redeeming qualities she might have been, but her death is so horrible that it might be very hard to feel any satisfaction over it.
The Blue Beast in Oh! Edo Rocket just wants to return home. Even though it is a ruthless killer that fed off humans for sustenance, it really just wanted to go home. By the final episode, it's been stabbed multiple times, using the last of it's life struggling to crawl along the ground, desperately reaching out and sobbing that it just wanted to go home. Actually very hard not to feel sympathy for it at that point.
Youya "Sakurako" Saiki from Sakura Gari. (Under spoiler tags since this involves a MASSIVE Shocking Swerve). Creepy Crossdresser who tortures people, clings to Souma and makes Masataka's life almost impossible... but he turns out to be an immature, broken, isolated child whose mind and heart splintered over his evil mother's death and his confinement, only realizes that he truly loves his older brother Souma when he thinks he's killed him, and ends up committing suicide.
When Shana finally manages to defeat Sorath and Tiriel, she takes a moment to feel sorrow. She notes that they may have been vile and incestuous, but their love was real and unconditional, and everything they did was to keep each other alive and happy, while she isn't even brave enough to confess her feelings to Yuji.
In the past, Sabrac's best friend Mare abandoned him because she couldn't stand how he was magnitudes more powerful than her. When Sabrac sees the Snake of the Festival, he's so distracted that Rebecca manages to knock him into the abyss. Bel Peol tries to rescue him with her Variable-Length Chain, but he declines. As he slowly disintegrates, he muses that he finally understands why Mare left him, now that he's met a being magnitudes more powerful than him. Remembering that Mare had been killed by the heroes earlier, he says they will be together soon, and the Snake of the Festival has finally made them equals. He tries to reach a nearby butterfly (butterflies being Mare's Animal Motif) but disintegrates before he can.
Lord Zarak (A.K.A. Scorponok)'s death in The Transformers. This could seem to not count, since he was trying to stop Unicron, and therefore not dying in a villainous way, but remember that he was the Decepticon leader at that point.
Moloch in Watchmen. It was made more poignant because, on many levels, it had more to do with Rorschach than him. This part:
Mr. Hyde in The League of Extraordinary Gentlemen singing "You Should See Me Dance the Polka" as he jaunts off toward the tripod is particularly emotional when it hits you that, for all his unbridled depravity, you'll never experience his brilliantly dark humor again. Throw in his unrequited love for Mina, and it gets exponentially more difficult to read.
It's also a bit difficult not to feel bad for Moriarty, given the horrifying manner of his death.
Asajj Ventress from Star Wars: The Clone Wars. She is given sympathetic qualities in the middle of the series, and her journey to sympathetic-ness is completed at the very end when her hero and mentor, Count Dooku, orders her shot to death because he can't be bothered to wait for her. She makes one last pitiful attempt to kill her nemesis, Obi-Wan Kenobi, and is cut down by Anakin. As she lays dying, she reaches out for Obi-Wan and tells him to watch the Galactic Core and Coruscant. Her final words finally reach this territory:
Obi-Wan: I thought you'd use your dying breath to curse us. Asajj: Perhaps I have...or perhaps I just...hate Dooku more than I hate you....Or maybe...you were right about me...all along....
When Destro was thought to have died in Marvel's G.I. Joe series, Snake-Eyes and Scarlett lay flowers at the place where he supposedly died.
Lady Jaye: You fight somebody long enough, you get to know them... and after a while— you start to respect them.
Transformers: Last Stand of the Wreckers: The Decepticon Snare, The Predators security director, is stuck at G-9 under one of the most sadistic Decepticons ever, Overlord. Despite him, and many other troops, disturbed and uncomfortable with everything note As security director he oversaw the torture and death of many Autobots, making it hard to scare or upset him, Snare throws a Spanner in the Works by freeing Impactor, and later leading some of the Autobot rescue team to save the rest of them. In the scuffle, he's shot and lays dying, asking Impactor to kill him before Overlord comes and finds what he's done. Impactor does so after thanking him.
Batwoman: Abbot, the werewolf leader of the Religion of Crime Cult. Throughout the series he saves Batwoman at least twice (though is at odds with her because he's a criminal who withheld information about her sister and was part of the cult that tried to kill her) and leads his troops into battle against Medusa's forces. Despite being afraid of Medusa and her power, he still chooses to stand with Batwoman, and tries attacking Medusa from behind. Medusa catches him, petrifies him, and shatters his body. Batwoman looks at his remains sadly, and later uses a piece of mirror to give Medusa the same fate.
Daken: The title character has done this twice. The first time, he broke down while dying, asking to see his father and apologising for placing a bomb at the Jean Grey Academy, before immolating himself with a bomb. The second, in which he inexplicably came back from the dead, involved him imagining how life could have been with his father and mother, had she not been murdered by Romulus. Wolverine is then forced to drown him to kill him, as by this point he is little more than a pawn for Sabretooth to use against him. Wolverine himself then breaks down, realising they could have had a happy life too. Considering Daken was The Sociopath most of the time... damn.
Discussed and subverted in Terra Obscura. The Grim Reaper was once a great hero, but turned bad and ultimately died while attempting to assassinate some old friends for the mob. At the end of the first miniseries, he's buried with the other casualties of the story in a hero's graveyard, complete with a marble statue of himself for a tombstone. However, none of the heroes attending the funerals believe he deserves it — it's just a political move to keep his actions from ruining their reputations.
Destruction. Despite being literally addicted to destruction, he was also the most sympathetic of all the draconequi, as he hated his addiction and wished he didn't have it at all. His desire in the war with the alicorns was to cause so much destruction he'd finally be rid of it once and for all. Him being killed and eaten by his own brother is extremely tragic.
Also kind of hard not to feel sorry for the Master in the Dark World, who the Valeyard subjected to the same thing Discord did to the Doctor (namely, being killed repeatedly with him regenerating each time). What's worse, according to Word of God, the Valeyard's claim to keep killing him until he gets a good personality was just an excuse to kill him over and over again.
Despite spending a thousand years massacring entire families with no remorse, following Discord's orders without protest, and generally being the biggest Jerkass in the Dark World, it's pretty hard not to pity Angry Pie when Twilight gives her a HUGE No-Holds-Barred Beatdown in "Cold Hoof Blues". By the end of the chapter, Angry Pie is crying and begging her foals to forgive her for failing to succeed in her task to bring them back to life. Even the other heroes (whom Angry Pie just tried to kill) are shocked and horrified by Twilight's actions. Thankfully, they manage to talk Twilight down and she ultimately redeems Angry Pie with a reverse Memory Spell (showing her Twilight's memories instead of her own).
Similarly, it's hard not to feel bad for Dark World Fluttercruel, even after all she's done, when she watches Discord get literally stabbed in the back by Rancor, which she simply cannot comprehend. She ends up crying and pleading with Discord to absorb her to heal himself. It shows that despite all else, she's still a foal who deeply loves her father and doesn't want him to die. What's she like by the end of the final fight with her? A broken little child who by that point knows her actions were wrong but is too driven by her Undying Loyalty to her father to make a Heel-Face Turn.
In the Pony POV Series Chaos Verse (a spin-off of the above), the death of Big Bad Nightmare Phobia invokes this. In her final moments, she recovers her lost memories and realizes just how in the wrong she was. Her last act is to reach out to Celestia and Discord longingly before dying. Luna even mourns for her afterwards.
Karin gets just enough time to ask Sasuke for a fake show of affection. Sasuke gives her a real kiss, and she dies in the middle of claiming that he really did love her.
After Gouki commits Suicide by Cop, his last words are to hope that his wife will be able to find happiness in the new world. Word of God says he died without knowing she was pregnant.
The immortal lion cub Shocker in The Lion King Adventures is a good example of this. Despite being a truly despicable character, his fate is rather harsh. He is buried alive, and, being immortal, is forced to choke on dirt for all eternity.
Films — Animated
In The Lion King II: Simba's Pride, Nuka, The Unfavourite, mostly just wants his mother to appreciate him. In the end, he dies trying to get her attention and fails even at that. He spends his last breath apologizing to Zira for failing, his death prompting one of the only displays of love and affection that Zira probably ever showed him.
The Princess and the Frog: Dr. Facilier spent nearly the entire movie trying to kill Big Daddy and enslave the souls of the entire city of New Orleans as a goodwill payment to his ''friends", and mode-locked Naveen into a frog, but if you don't feel even the least bit of pity for Doctor Facillier at the end of the movie, I worry you may not have a soul. He is, rather graphically, dragged into Hell by his shadow, screaming and begging the entire time. It's so bad that Tiana, whom he just put in a Lotus-Eater Machine and is the indirect CAUSE of his death, can only watch in abject horror.
In the Fantastic Mr. Fox, all the animals are saddened by the death of Rat, even Fox himself (who dealt the killing blow), despite his being the traitorous head of security for farmer Bean. In fairness, Rat did manage to come to his senses in his few final moments when he revealed that he had turned traitor because he had become too addicted to the apple cider of Bean.
Barbossa, but to a lesser extent, as he didn't have a Freudian Excuse, and in any case, he got better.
Subverted in the fourth film by Blackbeard. He's given the perfect chance to have such a moment by sacrificing his own life to save his poisoned daughter, but instead elects to Kick the Dog and save his own life instead. He ultimately dies anyway after Jack pulls a Poisoned Chalice Switcheroo. Plus, the aggressive gesture he makes towards his daughter seals the ambiguity of his relationship with her - as a loved relative or as a tool?
Lord Cutler Beckett gets a scene where his ship and crew are blown to pieces around him and he shows no fear, only devastation over losing all his allies and friends all at once.
Lord Beckett: "It's just... good business..."
The title character of Kill Bill goes out much like this when the Bride finally takes her revenge.
Taken even further in the book, as Frodo refuses to be upset with Gollum for what he did - even saying that without him, the whole Quest would have failed.
In The Mummy Returns, Imhotep is abandoned by Anck-Su-Namun — for whom he essentially damned himself in the first place — as he is desperately clinging to a ledge. For a moment, he can only stare at the O'Connells — Evie having just rescued her true love, Rick, from the same situation — with a look of absolute, crushing despair. Then, with nothing left to live for, he lets go of the ledge and allows what looks like the souls of the damned to drag him into the precipice. The novelization takes it even further. Rick, despite himself, actually tries to save Imhotep from falling into the abyss. Imhotep still lets go of the ledge, but not without a few parting words acknowledging that Evie and Rick's love for each other was the real deal.
Lady Deathstrike from X2: X-Men United definitely got such a send-off. Especially since her death was so painful looking and because she was Brainwashed and Crazy at the time. Stupid Stryker. She almost certainly wasn't evil. At one point, her eyes return to their normal (brown), non-brainwashed colour, and she looks around confused, clearly unaware of where she is. Stryker casually walks over to her, jerks her head forward, and applies the mind control serum to the hole at the base of her neck. She remains under control for the remainder of the film, with her eyes only returning to normal in the midst of her death scene.
Of course, it's All for Nothing in the end. What's the last thing Khan sees before he dies? Kirk and the Enterprise warping away to safety.
Shinzon from Star Trek: Nemesis. While not the best Trek villain, there's no denying that Shinzon's life sucked. He was created sorely to be a tool of war, and through no fault of his own, he was eventually condemned to a lifetime of back-breaking labor in a hellish mine (while a child, no less). And even though he managed to overthrow his captors and the entire Romulan leadership a decade later, his engineered lifespan ensured that he had a very short time to live. In short, he lived a short, violent, brutal life, and never really had any chance to know love or happiness.
The Penguin in Batman Returns. Even though he was a hideous psychotic sewer-dwelling monster, in his last few moments, he comes off as quite pitiable, and his burial at sea by his own beloved penguins actually comes across as rather moving. It should've been Narm, but it somehow worked.
"Shit... I picked the cute one." The scene is really an effective use of bathos using humor to accentuate the sadness.
What makes it really sad is that he spent the whole movie angry that he wasn't accepted. And it turns out he was.
Ironically subverted in Hitchcock's Strangers on a Train. Foe YayMagnificent Bastard Bruno is dying, and for a second it seems like he is going to admit his guilt; instead, he uses his last breath to further accuse the protagonist in front of the cops.
The eponymous character of Blacula. After watching his beloved Tina - the reincarnation of a woman he's waited centuries to see again - get staked through the heart, he deliberately walks out into the sunshine, killing himself.
The Rancor from Return of the Jedi. A dancing girl and a guard already had the misfortune of being its lunch. Luke has to work hard to avoid being torn apart by this hulking beast, and the spectators are very surprised when he manages to kill it. Then a fat, ugly man dashes out and cries as if Luke has just killed his pet puppy, and he's led away, weeping inconsolably. It's such an unexpected and well-played reaction that it was no longer just our hero slaying the dragon. Even this ravenous monster had someone who cared for it, and probably cared in return. This inspired writers in the Star Wars Expanded Universe, turning the Rancor into a Tragic Monster that was another victim of Jabba the Hutt's cruelty. It did have a good relationship with the fat guy, who was its trainer (and given a name, Malaki), and the reason why it ate most anything that was thrown into its pit was that it wasn't fed very often. Jabba also forced it to take part in a number of brutal fights against other dangerous creatures, and in fact before Luke came he planned to have it face off against a Greater Krayt dragon, something even bigger than it was. Malaki had plans of escape for him and the Rancor, but Luke happened to show up... And even after that, he never really had any grudge against Luke for it, blaming it all on his boss. (He wasn't the only employee of Jabba who hated him.)
HAL 9000 in 2001: A Space Odyssey. Despite being an apparently cold, logical computer AI who was willing to murder the crew of Discovery One, it becomes apparent why he did so: He was afraid. He did not want to be reprogrammed for making an error, which would essentially kill him. In the end, he is lobotomised while pleading for his life with the sole survivor (David Bowman), who ignores him. "Stop, Dave. I'm afraid. I am afraid, Dave. Dave... My mind is going. I can feel it. I can feel it..."
"My first instructor was Dr. Chandra. He taught me to sing a song. Would you like to hear it? Daisy, Daisy..."
The Stephen King movie Sleepwalkers looks like it's building to this, with the titular soul-sucking cat monsters constantly stalked by their weakness, and they're possibly the last of their kind. The young male Sleepwalker reads poetry describing their plight in class and seems to be falling for the female lead. A redemption plot looks all but guaranteed... And then when he tries to eat her soul, all the drama around whether or not he's falling for her vanishes and he becomes a gleeful monster with shocking speed.
Gen. Francis X. Hummel from The Rock. The fact that he was actually an Anti-Villain makes you feel even more sorry for him when he dies.
Sadako Yamamura, the Designated Villain from The Ring series, suffers a lot even before she becomes a villain. She is raped in the novels, lost her mother in both continuities, beaten to death by angry actors, and then she bonded with her evil twin and kills all those who harmed her before, including her own innocent boyfriend, before being tossed down the well by her stepfather.
In Ring 2, Sadako appears before Mai Takano and Yoichi Asakawa as a ghost, asking why they can escape the well and yet she cannot, before allowing herself to fall back down into the well for eternity.
Samara Morgan, the American version of Sadako, suffers a lot too and is thrown down a well by her adoptive mother. This doesn't help, since her biological mother tried to drown her as a baby. And then she gets trapped in the well again at the hands of Naomi Watts.
In Skyfall Raoul Silva is a former MI6 agent, who was tortured to the point of severe facial deformity and hinted-at PTSD to keep their secrets. M (who left him for dead) admitted he was a "brilliant agent", and he himself has pulled a Not So Different with James Bond. At the end of the movie, M has been mortally wounded, and Silva begs her to put the same bullet through their heads to end both their suffering.
In The Faculty, Casey kills the alien queen, Marybeth. As she is dying, he softly tells her, "You wouldn't have liked it here anyway.", acknowledging that — despite being a monstrous parasitic alien — she was just another outcast trying to find her place.
In Law Abiding Citizen, Aimes participated in a burglary. The plan appeared to be that his partner, Darby, would knock the adult occupants of the home to the floor with a baseball bat, then Aimes would handcuff them and then throw valuables from the home into a bag. Darby kills two people during the burglary while Aimes watches in horror and protests. Due to some legal technicalities and deals, Darby gets off easy while Aimes is executed. Aimes' last words: "What I did that day was wrong. But I'm not the one who killed those people. You're executing the wrong guy."
The death of Prince Nomak in Blade 2, who was driven to kill his father out of revenge for making him the first Reaper. In a final battle, he is stabbed in the heart and chooses to drive the blade in further to end his suffering. Tellingly, he does so with a smile.
"Strange … It hurts … It hurts no more …"
The Wicked Witch in The Wizard of Oz. She enters the film by spoiling the happy celebration of her family member's death, and exits wailing in pain as she watches herself melt to death. True, she spent the entire plot on a quest for power, but her actions are largely due to Glinda arbitrarily deciding that Dorothy should wear the ruby slippers, and halfway through the movie, the Wizard puts a hit out on her, technically making her the hunted party.
The Newborn in Alien: Resurrection. It was a murderous abomination, but unlike the aliens, shows some emotion, and acts as a naive and childlike creature. And its death was long and agonizing. Even Ripley 8 showed remorse for it.
Willie Lopez and Carl Bruner in Ghost. The scenes of them being literally dragged into the netherworld (not to mention what we imagine is waiting for them once they get there) are pitiful and terrifying.
It's hard not to feel a little sorry for the Emperor in Legend Of The Black Scorpion when he realizes he was just another pawn in the Empress's plan, and accepts death at her hands because "if it is your will, how can I refuse?" He dies in her lap.
Barty Crouch, Jr. Sure, he became a death eater, but all he ever wanted was a loving father. Some fans thought that when he received the dementor's kiss, that his punishment was not only too far, but also very sad, considering how neglected he was by his own father.
Peter Pettigrew may be the most disgusting and loathsome character with no excuses, but you feel a bit bad that his own hand strangles himself to death because of his one moment of mercy for Harry.
Nearly every book in the Redwall series uses this trope, and half the time, it's the Big Bad!
Martel's death in David Eddings' The Elenium fits the bill. After three books of playing Worthy Opponent to Sparhawk, he admits he knew Sparhawk was better all along, and both Sparhawk and Sephrenia forgive him and give him their blessings. Just for a minute, the guy who betrayed the entire Pandion Order goes back to being Sparhawk's brother in arms again.
Martel: You always said I'd come to a bad end, little mother, but you were wrong. This isn't so bad at all. It's almost like a formal deathbed. I get to depart in the presence of the only two people I've ever really loved. Will you bless me, little mother?
Similarly, Zedar's fate in The Belgariad makes one almost feel sorry for the guy. Sealed up in the ground, forever? Yeesh.
Worse when you consider that his Face-Heel Turn was a result of being forcibly turned by the Big Bad, and not of his own volition.
Speaking of which, said Big Bad also gets an Alas Poor Villain. Torak was a God of Evil, a Narcissist, and an utter bastard, but his death at the end, screaming for his mother as burning tears pour of his eyes after Garion takes away everything that matters to him? It's not pretty and it's acknowledged in-universe as such. The same could be said for Asharak, whose awful death will likely haunt Garion for the rest of his life.
There's a retroactive example in The Malloreon. Taur Urgas, King of Cthol Murgos was a frothing madman, and was played as such in the The Belgariad. In The Malloreon he comes off even worse as we find out what life in his home was like for his children. Garion notes when talking about the terminally-depressed 'Zakath that he would much rather be fighting Taur Urgas ("now there was a man I could cheerfully have gone to war with. He polluted the world just by living in it.") And then Eriond points out that "he was insane, Garion, and that's not his fault." At that point, all of Urgit's comments about his father's fits of madness and irrationality come back to you in a whole different light, as you realise that the man was genuinely clinically insane, and not merely Ax-Crazy, and never got any help for it.
Tigerstar, at least in the first series. Firestar notes afterwards that he could have been a great and noble warrior if he hadn't let ambition control him. The truly horrible death he suffered: being ripped open, and subsequently bleeding to death NINE TIMES.
From Codex Alera, for all the horror she had caused, all the death and the near destruction of the world, the Vord Queen seems, in the end, to be a sad, lonely child seeking the approval of her father.
Smug Snake Yuan Shu dies as a result of some mixture of illness, starvation, and dehydration, all the result of his last botched campaign. His last words are a request for a little honey water for his throat, to which his chef replies that there is no water in the camp, save that which is tainted by blood.
Ineluki, the Big Bad himself, is revealed to have committed all the atrocities in his life out of love for his people and a desperate desire to lead them to salvation. In the end, this realization leads directly to his defeat.
Utuk'ku, the Norn Queen and The Chessmaster behind Ineluki's rise, is broken by the failure of the Evil Plan, and is left as nothing more than what she always feared to become: a frail old woman.
A Dragonlance universe short story has Tanis and Flint kill a Black Mage who's been sucking the life out of people. After he's dead, they find out that he was doing it to prolong the life of his sickly son.
Test of the Twins: the Archmage Raistlin Majere attempted to become a god by dethroning one of the current ones. He manipulated everyone around him, abandoning or killing them as soon as they stopped being useful, and, as shown in an alternate would, have not only succeeding but have DESTROYED every other god in the pantheon, leaving him sole ruler of the universe. However, he sacrificed himself to save his time-traveling brother, ex-friend, and one of the people he manipulated, because they showed him that he would destroy the world in the process of attaining godhood.
Several villainous characters by John C. Wright are pitiable when they die:
War of the Dreaming: Angelo Casselo, who knows he's nothing but a pawn in the game; and Manannan, alias Tom, a What Measure Is a Non-Human? who had been desperately playing both sides in an attempt to prevent his people being annihilated.
Almost every half-blood villain in Percy Jackson and the Olympians gets this in the final book. Luke tries to kill the heroes multiple times and tries to help the Big Bad, Kronos, rise again (eventually hosting him in his own body). In the final chapters of The Last Olympian, he sees Annabeth bleeding, breaks free from Kronos's mind control, and realizes that he was fighting for the wrong side. He then kills himself to destroy Kronos, and it is indicated that he goes to Elysium in the afterlife. Ethan Nakamura fights in a battle to the death against Percy, and when Percy wins, he refuses to kill Ethan. Ethan repays him for this by betraying him and pledging himself to Kronos, enabling Kronos to rise again. Throughout The Last Olympian, he is seen working for the Titans. Then, Percy convinces him to turn against Luke/Kronos, who kills him, earning him sympathy in the end. Silena Beauregard originally seems like a gentle, romantic daughter of Aphrodite. However, she is secretly a spy for Luke, and the information she has reported has lead to the deaths of many campers. When Kronos and his minions become responsible for the death of her boyfriend, she begins to think twice about her actions and eventually disguises herself as Clarisse, rallies the absentee Ares campers, and charges a Drakon, resulting in her death. Her secret - that she was the spy - comes out as she is dying, but the other campers remember her as a hero anyway.
Olivia closed her eyes. This was no longer battle, but butchery, frantic, bloody, impelled by a hysteria of fury and hate, in which culminated the sufferings of battle, massacre, torture, and fear-ridden, thirst-maddened, hunger-haunted flight. Though Olivia knew that Shah Amurath deserved no mercy or pity from any living creature, yet she closed her eyes and pressed her hands over her ears, to shut out the sight of that dripping sword that rose and fell with the sound of a butcher's cleaver, and the gurgling cries that dwindled away and ceased.
In Dracula, Renfield's death invokes this trope. He's mostly unsympathetic for most of the novel—he nearly beats a man to death and attacks one of the protagonists with a knife—but when he realizes that Dracula had lied to him, he attempts to defend Mina Harker from him and is fatally injured because of it. The graphic description of his injuries doesn't help.
In Skulduggery Pleasant: Mortal Coil, the death of the Russian assassin Tesseract. After being fatally injured by Lord Vile, Tesseract removes his mask and asks Skulduggery to help him get outside so that he can feel the sun on his face one last time. As they go, he talks about how he'll miss his cat, and how he has no regrets.
"I have a cat, you know. Back home. [...] She doesn't have a name. She is just Cat. She curls up on my chest whenever I sit down, and goes to sleep. I hope she doesn't miss me. I'm going to miss her."
Mandrake is introduced in Duncton Wood three chapters in as a bloodthirsty, giant mole that later becomes an iron-fisted dictator. Then, in a quick moment of Rebecca's life, he scolds her for enjoying the snow and, after that, delivers a speech against the snow that's quite pungent considering his story. And when he finally dies, he does so half-mad from wandering the Ancient System for months alone, crying for his only daughter while being mercilessly beaten down by a revengeful Stonecrop.
Sly Moorcock from Stark by Ben Elton is a ruthless billionaire who has no qualms about leaving Earth with the other billionaires and letting humanity die in the inevitable ecological breakdown. Yet he moves more and more into Anti-Villain territory as the story progresses, and shows himself in possession of both moral standards and the capacity to love, and when he commits suicide in the epilogue by throwing himself out of an airlock, it is just as sad as when one of the good guys die.
'Wait,' she said, her voice weak and somehow very young. She didn't look like a mad faerie sorceress now. She looked like a frightened girl. 'Wait. You don't understand. I just wanted it to stop. Wanted the hurting to stop.' I smoothed a bloodied lock of hair from her eyes and felt very tired as I said, 'The only people who never hurt are dead.' The light died out of her eyes, her breath slowing. She whispered, barely audible, 'I don't understand.' I answered, 'I don't either.' A tear slid from her eye and mixed with the blood. Then she died.
In Good Omens, the demon Duke Ligur is doused in holy water in a booby trap set up by Crowley. He thoroughly deserved it, but for a demon, it's an amazingly horrible way to die, and his partner-in-crime Hastur immediately goes into Villainous Breakdown and attempts a Roaring Rampage of Revenge on Crowley, chasing him down a phone line.
Phoena's death in Fusion Fire was so horrific that Brennen did his best to comfort her in her last moments, despite the fact that not only was she responsible for his capture by the Shuhr, but she also tried to have him and his wife essentially tortured to death.
The third Safehold book, By Heresies Distressed, has this happen with Prince Hektor of Corisande. He's been beaten, he knows it, and he is preparing to negotiate terms of surrender with Emperor Cayleb. Before he can, however, he and his eldest son and heir are victim of an assassination that is blamed on Cayleb. Hektor, in his final moments, realizes that he truly loved his son, who had thus far been The Unfavourite.
In The Bartimaeus Trilogy, Faquarl achieves the vengeance he's been craving for 5000 years, and discovers that it doesn't bring him the satisfaction he wanted. Then he finds Bartimaeus sharing a body with a human, proving him wrong about the inevitability of conflict between humans and spirits. Bartimaeus narrates that he's never sure if, had he wanted to, Faquarl couldn't have killed them before they shot him.
Faquarl: Your discovery is remarkable. But it comes too late for me.
In Death series: this has happened with some of the murderers after they get caught or killed. Portrait in Death has Eve and Peabody realizing that the murderer they caught wasn't greedy, vicious, or downright evil, just pathetic.
Time Scout's Skeeter Jackson truly feels sorry for what happens to the enraged gladiator who spent the entirety of Wagers of Sin trying to kill Skeeter.
Antrax in The Voyage of the Jerle Shannara was just following its programming. Its reaction as it slowly loses contact with the outside world and shuts down is as sad as it is necessary.
The Aeneid: Most of the antagonists go out rather sadly. The standout may well be Mezentius, Nay-Theist, exiled tyrant, and brutal fighter whose disdain for the gods and vicious rule over his old city-state have brought him to Italy to fight as a mercenary. When his son and Morality Pet Lausus is slain, Mezentius goes ballistic, cutting down opponents left, right, and centre before being stopped by Aeneas; his Famous Last Words, wherein he refuses to pray and asks only that he buried by his son, are quite touching.
Durza, the Shade from Eragon, surprisingly earns sympathy just before his death at the hands of the protagonist. While fighting off the Shade's mental attacks, Eragon accidentally breaks through into his mind and sees a quick succession of images from his early life, before he became a Shade. The man who became Durza was originally a young orphan named Carsaib who was taken in by a sorcerer and instructed in the art. When his master was murdered, the grief-stricken young man called upon powerful spirits to get revenge, but they proved more than he was capable of handling and possessed him. Durza was pure evil, but Carsaib was a tragic figure who made a terrible mistake and paid dearly for it.
Of all the characters who are involved in the Final Solution of Timeline-191 — or at least all of the ones we get to know — only Hipolito Rodriguez is still human and moral enough to have a Heel Realization and repent of what he has done. It's the sincerity of his horror and repentance that evokes sympathy.
In The Stand, the death of Harold Lauder. Presented to us as a fat, sometimes disgusting social outcast who uses overly purple language at times, is insanely jealous of Frannie Goldsmith, incredibly hateful towards the Free Zone Committee (and Stu Redman in particular, whom he believes stole Frannie from him), pompous, contrary and argumentative, Harold is nonetheless a tragic figure: sadly used by the Big Bad, Randall Flagg, who takes advantage of Harold's weaknesses and literally leaves him to die by the side of the road with his leg shattered. Harold's final statement says it all: "I was misled."
In The Dark Tower there is the death of Trampas, one of the Mooks guarding the Devar-Toi. He works for the Big Bad, but he's actually a pretty decent guy once you get to know him. It's made pretty clear that Ted really doesn't want to kill him and even yells at him to get out of their way, although he is forced to eventually resort to throwing a mind-spear at him, killing Trampas in the process.
In Fate/Zero, Caster having a hallucination of Jeanne d'Arc reaching out to him while smiling and realizing just what kind of monster he has become before dying.
There is also Kayneth's death, based on your definition of "villain" (he did kill Risei). It's hard not to feel a little sorry for him when he gives up the War to ensure the safety of the woman he loves, only to be ruthlessly gunned down together with her.
The gamebook Search for Dinosaurs: A T-rex slowly starving in the aftermath of the meteorite fall is a rather pitiful sight, even if it tried to eat you previously.
Kara no Kyoukai: Overlooking View has Kirie Fujou, who unconsciously uses her spiritual counterpart to drive other girls into suicide out of loneliness. When Ryougi kills her spiritual counterpart, Kirie says that the moment Ryougi killed her was the most she has ever felt alive. Feeling she has nothing to live for and wanting to experience death again, she commits suicide.
There is also Fujino Asagami in Remaining Sense of Pain, although she's mostly an Anti-Villain. She's been raped, her own father has hired Ryougi to kill her, and she's dying a slow, excruciating death via untreated appendicitis. At the end of the chapter, she's crawling through rubble, weakly repeating that she doesn't want to die between bouts of vomiting blood.
Araya Souren in Paradox Spiral. As he lays dying after Ryougi defeats him, Touko questions his obsession with the Spiral of Origin. Araya recalls his past and we see that witnessing endless death and tragedy has left him guilt-ridden over his inability to save the people around him in his years as a wandering Buddhist monk, so he decided to at least record their deaths and desperately attempted to find some form of meaning or purpose in them.
Although the death of Bertha Mason in Jane Eyre leaves Jane and Rochester free to get married, it's hard not to feel for her, especially since her life has been so loveless and painful.
Loathsome as Grima Wormtongue might have been, it's hard not to pity him when one sees the level to which he has been reduced by the time of his death.
Lex in the appropriately named "Requiem". Clark arrives and scatters his ashes in the wind after he is blown up by Toyman's bomb planted by Oliver.
Davis Bloome/Doomsday in "Eternal", with Chloe crying next to him outside his cage. It would have been a bigger tear jerker if you don't know he is going to be back. By the time of his second death, he is a lot less sympathetic.
Also, that one Dalek, from the episode of the same name. Never has the word "Exterminate" been uttered with such pathos.
Cassandra in "New Earth".
Oh man, that poor Krafayis from "Vincent and the Doctor", an invisible alien that kills a child in its first "appearance". Who gets the blame? Vincent. And yet, later, after Vincent manages to fatally stab it with hiseasel, we find out that this particular Krafayis was actually blind, and its supposed "attacks" were just fearful acts of self-defense, having been abandoned and left all alone on Earth by its pack (according to Eleven, it even gasps out "I'm afraid" repeatedly in its last moments). The Doctor realizes this as it's dying and tries to soothe it, even though he can't evenseeit. Cue tears.
Yvonne Hartman, upon her final scene as one of the Cybermen, fighting off all the other ones.
The Minotaur in "The God Complex". Spent the whole episode "feeding" on the faith of those trapped in the hotel, but at the end, was revealed to be just another Death Seeker.
Doctor(translating the Minotaur's grunts): "an ancient creature drenched in bloodshed" (...) "for such a creature, death would be a gift." Actually we find out, in the very next sentence, that it was referring to the Doctor, but still... it makes sense in the context.
Angel's villains go out this way from time to time, which is natural for a show that swims in the Grey area. Nearly all the major antagonists get taken out this way, and it's up to the viewer to decide whether or not their fates were just. Darla, Lindsey, and Lilah each had ridiculously sad and depressing death scenes, while Holtz and Jasmine began to show signs of this trope, but would then yank it away by either setting into motion their own death or by tossing Angel off a bridge and then kissing him to screw with Connor, respectively.
Livia, the Evil Matriarch of I, Claudius was so pitiable on her deathbed that even Claudius, who knew her murderous nature well, was touched. Caligula on the other hand...
Caligula: And what makes you think that a filthy smelly old woman like you could become a goddess?
Caligula himself died a rather pitiable death. It must be quite a shock to discover that you are not immortal after all.
All the villains of I, Claudius qualify: Tiberius dies asking for lamb cutlets, Messalina frantically begs the soldiers sent to kill her not to take her head, and Sejanus (possibly the most despicable villain in the whole series) asks what has become of his children (both dead, and his daughter raped first because it was against Roman law to execute a virgin).
Another was Dr. Richard Daystrom, whose Motive Rant about being laughed at behind his back and underestimated is legitimately heartbreaking. The fact that Daystrom is portrayed by William Marshall - an amazingly talented black actor who was undoubtedly kept out of roles by racism - adds an excruciating Reality Subtext.
Dollhouse has a prime example of this in one of its final episodes, when Boyd is wiped, strapped up with explosives, and sent in doll state to destroy Rossum HQ. The doll stock line "I try to be my best" clinches it.
He's a certainly a lot less antagonistic than the other villains in the series, but Sano/Imperer's death in Kamen Rider Ryuki is no less heartbreaking. In summary, Sano had finally attained a semblance of the happiness he'd always wanted, only to be betrayed by a man he thought was his friend and left to dissolve in the Mirror World with no hope of returning home. "I only wanted to be happy", indeed.
In Kamen Rider Kabuto, we get the Rich Idiot With No Dayjob Tsurugi, who has thoroughly become a lovable comic relief character... until it's discovered he's really the Scorpio Worm. The real Tsurugi's over-the-top personality had over-riden the Worm's, essentially Becoming the Mask. While it seems like Tsurugi has betrayed humanity, even his potential love interest, it's actually all a part of a gambit to lead the Worms to ruin by following his orders. And it succeeds. Every Worm is defeated. Every . Worm.
Jiiya: Master! Tsurugi: Hey, Jiiya? Jiiya: What is it? Tsurugi: Is it okay for me to dream? Jiiya: Yes! Don't worry about anything. Jiiya will always be by your side. Tsurugi: Thank you, Jiiya.
LOST: The Man In Black. Once you learn his tragic backstory and motive, you can't help but feel sorry for the guy.
Captain Sawyer of Horatio Hornblower. Cruel towards his lieutenants and especially Midshipman Wellard, unstable, and antagonistic, but you can't help but pity the man who used to be a hero of the Nile. His death comes as both a relief and a tear jerker, especially as, directly beforehand, he had momentarily regained a shred of sanity, and he and Wellard had faced the escaped Spanish prisoners together with dignity.
No matter what you thought of Shane Vendrell after he murdered Lem in Season 5 of The Shield, you can't help but feel sorry for him when he killed himself (and his family) in the series finale.
NCIS: in-universe example: Ari. Ziva is clearly affected by killing him, she sings a song over his body and is haunted by it. Justified, they are half-siblings. The fans probably didn't feel the same way.
In Power Rangers Lightspeed Rescue, Lokai is killed by Queen Bansheera, who forced Diabolico to fire upon the Rangers while he was fighting them. As he lay dying, Lokai lamented that all his years of faithful loyalty to the treacherous monarch seemed to be nothing but a waste.
Power Rangers Samurai: Deker is freed of his curse after his final duel with Jayden, and is finally allowed to ascend to the afterlife after being forced to live with a hunger for battle for centuries. Even after all that he did in his battles against the Samurai Rangers; seeing him go was genuinely saddening.
Even more so Dayu, Deker's wife who was cursed alongside him and had to live with a beloved husband who no longer remembered her. At Deker's death, she fell into despair at her lost love and the years she spent pining for him. She then lost it, denying her human side and swearing utter loyalty to Master Xandred, who killed her and absorbed her body. At least Deker died happy.
Queen Beryl in Pretty Guardian Sailor Moon. The real motivation behind her attempt at awakening Metaria and ruling over the world? She wanted to get back at Princess Serenity who always had everything she dreamed of: fame, beauty, power, and, most of all, Prince Endymion's love. 'Why do you... take everything away from me?'
The Salamanca twins provide an interesting subversion. They go out in a particularlyinhumane fashion and are still treated as the irredeemably evil force they have been up until that point, but that scene served as the climax to an episode that opened with a flashback to their Freudian Excuse.
Nick Cutner in Being Human. Especially after the flashbacks. He was just desperate for approval from people who treated him so horribly, including Hal. In the scene where the Old Ones utterly cut him down his down his devastation is heartbreaking. Then he gets cooked.
With the tendency for The Amazing Race teams to get a touching send-off after being eliminated or losing, even teams people originally rooted against can invoke this response upon realizing just how passionate they were about the race. The biggest example is probably Season 2's Wil, whose final speech has him tearing up and trying to figure out what he could have done better, while his ex-wife Tara celebrated with the winners, one of whom she had been flirting with for the entire season.
Charmed: Lulu and Frankie, the ghosts who possessed Cole and Phoebe in "Paige from the Past". Despite being villains, you can't help feel sympathetic when it's revealed that their entire Unfinished Business was simply wanting to get married. Considering that they'd have likely moved on afterwards, Piper interrupting the ceremony comes across as kinda a dick move on her part. Of course, sympathies are lessened somewhat by a line of dialogue that reveals that along with being robbers, they were also serial/thrill killers.
Stringer Bell's downward spiral and death is seen as this by many fans of The Wire. Despite him being a murderous drug dealer who setup D'Angelo Barksdale's death and then had an affair with his woman afterwards, Stringer Bell was also shown as a thoughtful man who wanted to leave the life of crime and become a legal business man. He ends up getting screwed over by Senator Clay Davis when he tries to go legit, and his scheming finally catches up with him, to the point he can no longer talk is way out it. Finally, he decides to Face Death with Dignity.
In Ravages Of Time every single dead villain receives at least a chapter as an eulogy, making Yuan Shu and Lu Bu look extremely sympathetic.
Makuta Krika in BIONICLE; he was the Noble Demon of the Makuta with a Monster Sob Story, who only went along with the plan of the Makuta of Metru Nui because he saw it as a "damned if you do, damned if you don't" scenario. He made a genuine effort to help the Toa (the heroes) at the end of the Karda Nui arc, and then, when he learned that the Makuta were about to outlive their usefulness, he tried to warn them, and was rewarded by slowly becoming so intangible that all of his atoms flew apart - the kicker of his death was that it was caused by his own power being forced out of control by his brethren, who thought he was lying.
Subverted in Oklahoma!. Curly tells Jud that when he dies, people will cry for him despite being afraid of him prior to his death. When he actually dies, what's the first song that they sing? "Oh what a beautiful morning..."
Foreshadowed in the Curly/Jud duet Poor Jud is Dead. Jud is really getting into this vision of how awful people will feel when he's dead, and Curly is echoing:
Jud: And folks are feeling sad that they used to treat him bad, and now they know their friend is gone for good. Curly: Good.
Tybalt. After all, the hero had just murdered him for what had ultimately been an accident. As this is Shakespeare, the validity of this is really up to the director andthe actor.
Paris would also be a good example. He's often displayed in a negative light, but ultimately, is simply a man trying to woo a girl he's in love with in the typical fashion of that era, and he's killed while trying to arrest a dangerous criminal who had killed the cousin of the woman he loved, and, for all he knew, drove her to suicide.
Trevor's death. On the other hand, one might not feel so bad about killing Trevor when you remember some of his actions... But being burned alive, screaming his head off, is a horrible way to die even for him. That Trevor's implied to be more surprised and hurt by Franklin's betrayal than anything else is rather heartbreaking on its own; he clearly trusted him completely.
Michael's death, as well. From Michael's distraught voice as he screams how Franklin was like a son to him, and that Michael practically let him stay at his house, to the shot of Michael's corpse on the ground and Franklin looking like he's just fighting back tears when he sees what he's done.
Although Durandal from Marathon is not technically a villain, he is forcing people to die meaninglessly, and sends the player on suicide missions, sometimes for the hell of it. Tycho also reveals that Durandal doesn't care about humanity or the S'pht (in fact, he might hate humanity, although this may be somewhat a case of Unreliable Narrator), he just wants to find the Eleventh Clan of the S'pht because he believes that they know where he can find the Jjaro, who have the ability to help Durandal become God in the next universe. Nevertheless, he did want to stop the Pfhor invasion of Earth, and killing him was a horrible thing to do. Until we find out that he wasn't really dead.
Most of the bosses in the Metal Gear Solid series gets this, including Psycho Mantis, Vulcan Raven, Sniper Wolf, Fortune, The End and Vamp.
Solidus's defeat was also somewhat pitiful on his part: He ended up killed by the Patriots via Raiden, after working hard to re-establish America as how the Founding Fathers founded it with liberty, especially when he had nothing else to leave behind other than this. This is best demonstrated by his final actions: After falling from Federal Hall, his last visible action is him reaching up to a statue of George Washington in longing, as he attempted to redo America the way Washington originally founded it.
The kicker though, has to be every single member of the Beauty and the Beast unit from number 4. And if their respective backstories didn't solidify their position as the official Woobies of the game, their death scenes, where their humanity finally shows through, are a pretty good litmus test for deciding if there is an ounce of humanity in you.
No sympathy for Zero? Yes, he's the cause of the events of the series (albeit indirectly, it's hard to be responsible for the actions of your AI constructs when you've been brain-dead for most of their reign), but he truly meant well and it just didn't go right. By the time we see him in 4, he's a pitiful old vegetable who can't even take responsibility for the things he didn't know he caused.
The Quirky Miniboss Squad from MGS is even more this trope for a lot of people who've read The Last Days of Foxhound. Sure, it may not be canon, but it does a damn good job of characterising them all in a sympathetic manner, even Liquid himself.
Sniper Wolf is the straightest example, purely through her canon depiction.
The Boss' killing. Until a minute later, you really feel this. After that, whatever humanity there was just gets strained as you learn the truth. Considering how well it was done, it may still be a poor villain because of how well the boss played her roll.
Axel from Kingdom Hearts. The fact that he jokes about his death makes it worse.
Sora: You're... you're fading! Axel: That's what happens when you put your whole being into an attack... not that Nobodies actually HAVE beings, right? Hehahahaha...
Even Saix gets a pretty touching sendoff. "Kingdom Hearts... where... is my heart?" Indeed, nearly all of the members of Organization XIII get touching sendoffs (eight out of thirteen, the exceptions being Xemnas, Xigbar, Xaldin, Zexion, and Marluxia), which is one reason why they get the Draco in Leather Pants treatment.
Vexen: I don't want to... go yet... Lexaeus: Forgive me, Zexion... Demyx: No waaaaaaay! *Sob!* Luxord: How could you... Roxas? Larxene: I'm... fading? No, this isn't... the way I... I won't ALLOW...!
It's been implied, though, that all of them have been reborn, and confirmed for most of them (though Xemnas is still a Big Bad and Saïx is still The Dragon).
Xemnas: I need... more rage... I need more... hearts... Sora: Xemnas. There's more to a heart than just anger or hate. It's full of all kinds of feelings. Don't you remember? Xemnas: Unfortunately... I don't.
And it's not just the Organization. A certain Artificial Human got a heartbreaking farewell...
Riku Replica: So... it's over. Hmph. Death doesn't frighten me. Good riddance to a phony life. My heart was never real. I'm sure even what I'm feeling now is probably fake. Riku: What are you feeling? Riku Replica: What happens when a fake dies - one like me? Where will my heart go? Does it disappear? Riku: It'll go somewhere. Maybe to the same place as mine. Riku Replica: A faithful replica until the very end. That's... okay.
And now we have the death of Xion. As if the events leading up weren't wrenching enough, then comes the Ret Gone...
Roxas: Did I... do this to you?
Vanitas' death might be the most impressive example of this in the whole series — in spite of being made of darkness,the expression he makes right before he dies◊ is so lost and sad that it's hard not to feel bad for him. It doesn't help that his face is identical to Sora's, apart from the eye and hair color.
This actually happens to one of the Disney villains. While the rest of the villains willingly allied themselves to The Heartless for their own sick desires, Clayton was just a hunter who happened to be in the wrong place at the wrong time and having an emotional moment of weakness, which allowed the Heartless to find him and steal his heart, turning him into their puppet. After his death, the party expresses pity for him, with Tarzan even saying that if Clayton had some friends at his side, then maybe he wouldn't have fallen to the darkness.
Tarzan: Friends, same heart. Clayton, lose heart. No heart, no see friends. No heart, no friends.
The Fire Emblem series in general is quite fond of this trope. More specifically:
Orson also qualifies. Despite betraying his homeland of Renais to the Grado forces, it's made clear that he only did it because the death of his wife broke him completely, leaving him open to manipulation by having her (half-assed) resurrection offered in exchange for his compliance. He becomes more physically-emaciated each time he appears, and in his last appearance (where you kill him), he's gone completely off the deep end talking to a shade of his wife - his last word is her name. Ephraim, Eirika and Seth all show sadness at how far he fell, not able to bring themselves to hate him despite all that he did.
Fire Emblem 6 has Gale, who was never your enemy, and was possibly romantically linked to one of your party members (though it isn't necessary to kill him) and Brenya in the bonus chapters - fighting for a king already dead and knowing she only fights to be killed to stall your army. The final boss was a frail looking girl, though she gets better.
Despite being a veritable madman, King Zephiel - his final words, which verify his adamant belief that Humans Are Bastards is quite sad, particularly in light of the kind boy he used to be before his father's repeated assassination attempts screwed him up. Not to mention Murdock, who goes out loyally serving him despite being an honourable man who disagrees with the war as a whole.
All the major Black Fang members. Brendan, Uhai, Ursula, Darin, and yes, even Nergal himself, whose death becomes more pitiable depending on how many bonus chapters you unlock. The only Fang members you can completely hate at the end of the day are Psycho for Hire Jerme, Church Militant Kenneth, Evil Matriarch Sonia, and Ephidel, who probably has the most satisfying demise in the game.
And Kenneth and Jerme might earn a modicum of pity as well when you consider their appearance as Morphs in the finale chapter, Go Out with a Smile included. It is implied by Eliwood and Co. that both men were driven insane by Nergal, especially when you consider that Jerme used to be the Fang's finest assassin before Jaffar joined the Four Fangs - Brendan had already shown he didn't tolerate sociopaths by locking up PascalGretzner (who deserves to be on the list of 'completely hateable Fang members') in the past, after the man massacred innocents while gunning for his targets, just because he enjoyed killing so much.
Another is Nergal's top lieutenant, Limstella. Despite being a rather creepy, emotionlessArtificial Human, she has an absolutely gut-wrenching final moment: "I am not human. This body and this heart are constructs. Yes, as is this sorrow."
Back in Fire Emblem: Seisen no Keifu, several people Tear Jerked over Alvis, who was actually similar to Lyon, and wasn't entirely the evil bastard he would appear to be if you took him in context. (One Freudian Excuse later) He was actually shown to be trying to ''stop'' the Child Hunts that were going on. Even Celice, whose father was murdered by Alvis, later says that Alvis does not deserve to be demonized in history.
The remake of the game adds Kleine. Throughout the game, she's depicted as a sadistic, cold-hearted killer, who constantly abuses her adoptive sister Katarina for being useless. So you look forward to the moment when you finally get to fight her...and her death comes as one of the most heart-wrenching tear jerkers in the series, specially when she asks Katarina "Stay with Me Until I Die".
Also, Eremiya from the remake. She's the one to blame for Kleine being the way she is (and Katarina, and Roro, and Roro's clones...), then when you finally beat the bitch, it's like a moment to celebra - what'sthis?! Gharnef put her under Mind Rape when she fell into despair after witnessing the deaths of the orphans she originally cared for during the war, turning her into a Mega-Abusive-Bitch? And now, while she's dying, he completely restores her memories of who she once was, laughs, and lets her bleed to death in complete despair? ...Ouch. Just...ouch! For a character who didn't even exist in the original game, that's some pretty powerful Jerkass Woobie material right there. There's a very goodreason Gharnef earns more loathing than the game's actual Big Bad, Medeus.
General Zelgius (Levail as well, for that matter) in Fire Emblem Radiant Dawn. Yes, Zelgius is the Black Knight who killed Greil, but you still can't help but feel sorry for the guy.
Then there's his boss, Sephiran, a Woobie, Destroyer of Worlds and Death Seeker who's out to end it all because he can't see the good in the world anymore. The latter's cohort, Dheginsea is another example, as is Jarod, who for a relentlessly unpleasant Jerkass gets a surprisingly sympathetic send off, going down fighting after giving a Rousing Speech to his troops. The previous game has Antivillains Shiharam and General Bryce, whose death's cross the line into Player Punch territory, and Petrine who while an incredibly vicious bitch for most of the game, goes out so terrified that it's hard not to at least pity her.
Optionally, Hetzel might get one. Of all the Begnion Senators, he's clearly the least evil. (e.g., buying Rafiel as a slave only to save him and then release him.) Even when you do fight him, he apologizes and says he doesn't want to do it, he's more afraid of what Lekain will do to him if he doesn't go along with it. Data that has been found suggests that he could have been spared, actually.
Grom Hellscream in Warcraft. Despite slaughtering his way across two entire planets, despite embracing demonic corruption twice over, despite condemning his people, and despite frequently jeopdardising the future of the Horde...his Heroic Sacrifice and death scene in Reign of Chaos makes up for it. Almost.
The final moments of Arthas Menethil in World of Warcraft surprisingly fit this. Despite constantly hearing that nothing remains of Arthas himself, there's still enough for him to cling to his father's specter in search of some final comfort as he lies dying. Somewhat eclipsed by the ensuing Heroic Sacrifice.
Given Illidan's official Woobie status throughout much of Warcraft lore, his death (by betrayal, no less) at the end of the Black Temple raid dungeon is tragically empty. What a Senseless Waste of Human Life indeed.
Baldur's Gate's Irenicus is rather pitiable in his final moments. Even more so is Yoshimo.
Darth Malak in Knights of the Old Republic. Despite setting up camp on the far side of the Moral Event Horizon, his doubt and regret as he's dying is just believable enough to earn a little sympathy. Bastila, too, if you decide to kill her (or have to because you can't talk her down, although less so there.)
Only if you take the Light Side choice. If he dies in the Dark Side choice, he just mutters that you are eviler than him, and he just doesn't measure up.
Many villains in the sequel - Colonel Tobin, Darth Sion, Atris, Kreia...well, maybe not Nilhius.
One of the original ones for Video Games was Oddler/Odd Eye in Shining Force II. Dude joined you as a blind kid with no memories, he follows you and clearly admires your skill, and stays behind with Creed. Unfortunately, he turns out to be a greater devil and is fought as a boss, wishing, as he died, that he could live his life again not as a devil.
After each of the mind-blowingly epic boss battles in Shadow of the Colossus, you are treated to a brief cutscene of the colossus succumbing to death accompanied by remorseful and heartbreaking background music. Surely enough, you feel like a sick, twisted bastard for killing such a magnificent creature.
In Mass Effect, this applies to Saren if you manage to convince him that he's been indoctrinated and become nothing more than a slave to the Reapers. He regains enough control to shoot himself in the head, letting him die as himself;
Saren: Goodbye, Shepard. Thank you.
Matriarch Benezia, as well, particularly since she started out trying to keep Saren from going too far and ended up Brainwashed and Crazy for her efforts.
In the sequel, the Collector General, when it's revealed that Harbinger has been possessing it all along. The way it looked around in confusion and reaches up at the hologram of Harbinger (because it's all it has), as the space station was blowing up around it just tears your heart out.
Although it's uncertain when, exactly, he fell, at the final moments of Mass Effect 3 you're confronted with an indoctrinated Illusive Man. He can either be made to realise this, in which case he shoots himself with a resigned, "I tried, Shepard", or he can be gunned down, following which he looks out, one last time, at the view of Earth and comments;
Illusive Man: There... Earth. I wish you could see it like I do, Shepard. It's so... perfect...
The supposed Luna VI that was actually an illicit AI called Hannibal gets one of these when you destroy the last of its mainframes. Sure, it had killed or was trying to kill everyone around it, but when you pull the plug the terminal fills with binary code that, if translated in real life, reveals the word "help" repeated over and over. Hannibal is scared of dying and is desperately shouting "Help me!" over and over as he fades away.
This is made even sadder by the revelation that Hannibal was rebuilt into EDI. She still has memories of it.
All of the God-Generals save Dist, who survives, in Tales of the Abyss get one of these. After the speeches they give about their ideals before their final fights (most of which involve copious amounts of angst), it really makes you feel like a douche for having to kill them. There's some Grey and Gray Morality in there, given some of them...
Arietta's might be the worst, however. She's one of the least malevolent of the God-Generals and has, at that point in the game, lost everything that matters to her...and unlike the other God-Generals, who mostly get fought in Boss Battles and then die off afterwards in cutscenes, she actually does die directly due to the player beating on her, her last words lamenting her failure to avenge the deaths of her mother and Ion, both of which are caused by the player party's actions. And she's only a little girl!
Sync tends to get this the least out of the other God generals (Sans Dist, since he never actually dies), mostly because he didn't seem to give as much of a shit about it all. Yeah, he's got some angst and all...but he psychologically tortures Anise and does all sorts of things that almost push on the Moral Event Horizon.
The game also does this to Grand Maestro Mohs.
On the subject of a Tales of game, Tales of Phantasia also has one of these. Which was the game's primary twist in the end, since Dhaos had stated in the very end that he didn't want to be ultimately confronted by the heroes since he was just trying to save his people. Even the characters say that they appear to be the bad guys from Dherris Karlan's point of view. Way to go, Cress.
Alice in Tales of Symphonia: Dawn of the New World. Most people absolutely despised her after all of the cruel things she did, treating Decus like crap when he is in love with her. After their final fight, Decus even takes Emil's sword for her and died in Alice's arms. She realized that she loves Decus after all, proceeded to go into an Unstoppable Rage to avenge his death. She even cried for him. Then, she said that soon they'd be together again and held his hand as she died.
This is following after a few Pet the Dog moments from her, too.
Even the first Tales of Symphonia had this with either Zelos (if you got the 'bad' ending), who pulled a Face-Heel Turn (in his last words, he's talking about how his death might make life easier for his estranged sister), or Mithos himself, who started this entire 'chosen' and got involved in the 'splitting the world/harnessing mana' mess because he wanted to bring his sister back from the dead. His last words don't help.
Mithos: Farewell, my shadow, you who stand at the end of the path I chose not to follow.
Poor Walter in Tales of Legendia. He was just doing what he was conditioned to do since birth.
One really couldn't help but feel sorry for Lambda after hearing all of the stuff that was done to him by Emeraude. Almost makes you feel glad for him when he blows her up.
Baten Kaitos Origins does this for almost every villain in the game, with the exception of the game's biggest monster and the one who was horror incarnate. This is particularly notable in the case of the Big Bad and his Dragon, both of whom had their daughters crying over their bodies as they died, but it also shows up in the deaths of the rest of the Five-Bad Band - such as Nasca, who fought despite knowing it was practically suicide simply because "Heughes would never let me live it down!" Then you get to Heughes... who does the same thing because running away would be a bad example to set for Nasca. Though technically, it's the player's choice whether or not to fight and kill Nasca, Heughes, and Valara. And if you choose not to, they each pull off different but equally awesome Big Damn Heroes moments at the end of the game.
Kefka: Why create when it will only be destroyed? Why cling to life, knowing that you have to die? None of it will have meant anything once you do. Terra: We live to protect what we hold dear. As long as you have that, you can find the meaning on your own. Kefka: Meaning, schmeaning. The whole world's going bye-bye! You included! Life... Dreams... Hope... Where do they come from, and where do they go? None of that junk is enough to fulfill your hearts! Destruction... Destruction is what makes life worth living! Destroy! Destroy! Destroy! LET'S DESTROY EVERYTHING!" *explosion, followed by a sobbing laugh*
The end of Final Fantasy IX had Kuja dying at the base of the Iifa Tree. Being a fluke with a crushingly short life-span made him cruel and nihilistic, but only when he was defeated by the heroes and had nothing left to live for did he realize too late what it means to really live. This also gets a callback in Dissidia.
Vayne is one of the most affable and - dare one say it - likeable antagonists in the series due to the inherent humanity behind his actions, and though he doesKick the Dog on occasion, he's a Well-Intentioned Extremistpar excellence with good emphasis on the "Well-Intentioned" part of that description. His genuine love and compassion for his cute little brother Larsa helps immensely.
In the case of Cid, it hits especially hard when the player realizes that Cid only started neglecting his family because Venat contacted him.
Venat exemplifies all the best aspects of the Satan Is Good trope - the compassionate Defector from Decadence to contrast with the Jerkass Gods, the genuine liking for mortals and a desire for them to attain self-independence (much like Prometheus), and the capacity for kindness when s/he sacrifices his/her immortality simply so that Vayne doesn't have to die alone; as such, they depart the world together and in some semblance of peace.
Final Fantasy Tactics: Wiegraf Folles and his sister Milleuda, who both started off well-intentioned and were arguably more heroic than the heroes during Chapter One. Wiegraf eventually went too far, what with joining the Corrupt Church and selling his soul to the Lucavi, but still...Milleuda, in contrast, was sympathetic until the end - being forced to kill her to progress in the game is a notoriousPlayer Punch.
Isilud Tengille, who wasn't even evil - when he realised he was on the wrong side, he tried to stop his father-turned-demon, only to be unceremoniously killed, followed by asking Ramza's sister Alma to send Ramza his apologies for having opposed him.
Both Confessor Zalmour Lucianada and High Confessor Marcel Funerbis had incomplete information, and seemed to genuinely believe they were doing the right thing. Zalmour goes out with a commendable dignity as he prays to God - not the Lucavi demons - to punish the wicked for their sins, and Funerbis swallows his pride as he begs Ramza "the Heretic" to stop the demons (after having been run through by the Big Bad and his minions despite pleading for his life).
The main (human) antagonist of Xenogears vowed to use science to create a God to replace the one who had created, and then abandoned, the world. In despair over the death of his unrequited love, Sophia, he succeeded in bringing "God" back to the world in the form of a malevolent alien superweapon. Upon its destruction and his own defeat, he was taken up directly to Heaven by the true God, while telling the reincarnation of Sophia and her lover that he envies their capacity for unsullied human love.
The main antagonist of Xenosaga exhibits this trope as well. After commenting positively about the fact that he will no longer have to fear losing anyone (a fear which was the catalyst for his decent into psychopathy to begin with) in oblivion, he tells the protagonist, whom he has known since childhood and who is clearly distraught by the climax of their encounter: "What's with that face? You look like... you just lost your best friend." The protagonist himself is on his knees crying at this point, and you should be too. Ironically, he cries out for the antagonist not to 'leave him alone', a sentiment the antagonist exhibited in childhood upon realizing that he was immortal and would outlive the people in his life.
BioShock: the Big Daddies. After you kill one, its Little Sister runs up to the corpse, crying and asking for it to get back up again.
The Alpha series, those bastards who attacked with no warning. You're going to feel like a true Heel when you learn the reason why they're so suicidal. They lost their Little Sister, who was their whole world. Later, you're treated to the fact that one of them spent the remainder of his life crying next to a Gatherer's Garden. Almost makes you want to kill them just to put them out of their misery.
And then there is Andrew Ryan. He is defiantly set up as the main antagonist during the first part of the game (he tries to kill you multiple times), but his death is too jaw dropping for words. At this point with he dramatically demonstrates that you have never been free and can be (and have been) forced to do anything with the phrase "would you kindly." He is obviously disgusted by this as it contradicts everything his Objectivist philosophy is for, summed up neatly in the phrase "A man chooses, a slave obeys." At this point he "asks" you to kill him, knowing fully that you're his own son, taken from him by his worst enemy and turned into an assassin. Though Ryan's motives are famously ambiguous at times (something others comment upon in game), it seems he sacrificed himself in order illustrate the PC's fatal flaw to him, shouting "A Man chooses. A Slave Obeys" again as you beat him to death.
Songbird in Bioshock Infinite who Elizabeth is forced to kill near the end to protect Booker, by transporting herself and Booker to Rapture, and Songbird in the water where the pressure crushes him. Elizabeth comforts him through the glass of Rapture and Songbird reaches out to her, before his eyes turn from red to green, indicating a peaceful state, as he dies.
Interestingly, Cave Story doesn't do this for the Big Bad, but for the little guys. In the standard ending, the cutscene features a slow pan over the various levels of the game and all the enemies in them, set to sad music. Then, the floating island they're on crashes.
Invoked in-game in Super Robot Wars Original Generations, as part of the Retcon given to Axel Almer. Originally, in the face of death, he continued to mock Lamia and died 'being a doll on his own will'. In the remake, however, after his heartfelt confession on how the Artificial Human surpassed his very low expectations, he mutters Lemon's name before his demise, signifying his genuine care; even Raul, who was practically angry at Axel, who caused Fiona to disappear, feels bad on having to kill him. Then, it's subverted in Original Generation Gaiden, when Axel comes Back from the Dead and has a Heel-Face Turn.
An even better example is Echidna Iisaki, one of Lamia's sisters. Thought to be personality-less as the W Numbers are suppose to be, in the end, she's revealed to be completely sentient when she disobeys orders to come back alive at all costs in order to take a fatal blow for her Mistress's boyfriend, Axel. When asked why, she responds that it would make her Mistress sad if Axel was killed, as, while she can be replaced as many times as needed, humans are gone when they die. Lamia begs her to eject so they can help her, but the dying Echidna defiantly proclaims "I am not... Echidna Iisaki! I... am... W16...". Axel's reaction on both occasions counts for this trope. While the original had him cursing over how a doll he hated saved his life, you feel sorry for Echidna dying and still being treated like trash by her superiors; the remake had Axel lamenting over how her death will end up demoralizing the whole Shadow Mirror army.
Kitaniji from The World Ends with You fits this well. He, upon realising he has failed to save Shibuya, leaves it in Neku's hands, accepting his fate for Shibuya's sake.
Walter Sullivan of Silent Hill 4. Spends the first half of the game brutally murdering everyone the player character meets and the second half trying to kill him while laughing hysterically, but it is still almost impossible to hate someone whose final action was to desperately call for his mother. By the end of the game, the player is really finding themselves wondering if you're killing him because you hate him or if you just want to put the man out of his misery.
Dark Knight Andoras in Tactics Ogre. All of 'em were jerks, sans Lans Tartare, Volaq (due to being Out of Focus, but what little we do see paint him as an honorable man), and maybe Ozma in the remakenote Only when she joins you. But then comes Andoras, who actually joins Barbas and Martym in betraying the other three, possibly for personal gain. So you'd probably think he was dislikable, like Barbas and Martym were. But he actually did it because his family and countrymen were enslaved by Lodis, and he wanted to get back at Lodis to free the countrymen he felt were "hostages". Before he dies, he even warns Denam that Valeria must be united, because that was the reason that the Bolmarkians (his nationality/ethnicity) and Nirdums (the Royal family he was a part of) fell to Lodis.
In the Gaiden Game, Rictor and Cybil come off this way. Shaher also only wanted attention from God, too.
For that matter, a lot of bosses give lines when they die, such as characters lamenting about how they couldn't give medicine to their sick daughter, how the boss was fighting for his wife, and how the wife of said boss was pregnant... Matsuno really wanted to drive home the point of how war affects everybody in terrible ways.
In Dragon Age: Origins, the moment when (if) Teyrn Loghain is executed is one of these, as his daughter weeps and begs for his life and he looks back saying that little girls never grow up and always have pigtails in their hair. Then she gets spattered with her own father's blood.
Iji's final boss, General Tor, gets a death scene like this.
Doctor Breen in Half-Life 2, who genuinely believes that what he's doing is the only way that humanity can survive. His Evil Gloating and attempts at Not So Different get increasingly desperate as Gordon gets closer and closer, and right before his death, he tearfully cries "You need me!"
This is made all the more tragic when it turns out that Genbu is defending his boss because she was the only warrior to accept him as a Ninja, despite his otherwise comically inept ninja skills.
The Front Mission series is known for having these type of sad deaths with most of its supporting cast.
Front Mission 3 is one of the better examples since you get to play two story lines which help show you the lives of those you end up killing or saving from new perspectives, including recruitable characters.
No More Heroes often invokes this with the deaths of each boss, many of them being sympathetic and all of them being awesome. Good examples include Dr Peace, Holly Summers, Jeane, Ryuji, and Captain Vladimir.
Alice Twilight certainly qualifies. By the time Travis meets her, she's sunk into depression, mourning the loss of Margaret Moonlight who she had some connection to, and honestly just wanted to die. She even spells it out to Travis that the reason most of the assassins he's encountered have been so delighted to meet him is because they all just want to be freed of the endless fighting. It's also her death that causes Travis to have a Villainous Breakdown/What The Hell, Hero moment as he finally gets sick and tired of the killing.
Thomas and George from Deadly Premonition. Thomas secretly had a crush on George, and was jealous of Emily over the fact that George obviously cared for her. This jealousy was used by Forrest Kaysen to drive him murderously insane, forcing Emily to kill him. As for George...you wouldn't think he'd get a touching sendoff, given his actions, but then you realize that he only did the murders because the horrificCold-Blooded Torture his own mother subjected him to during his childhood deeply traumatized him to the point that he wanted to become strong above all else. Oh, and like Thomas, he was essentially being used by Kaysen.
George's pitifulness is driven home during his Villainous Breakdown, where he tearfully calls out to his long dead mother, saying that it wasn't his fault and begging her to not to hurt him again...
In The Legend of Zelda: Twilight Princess, Link and Zelda also express pity as Ganondorf passes away, though that seems to just make him hate them all the more. His death blow is actually done by Zant, who was his servant and clearly turned on him, likely killing them both.
The final rank mission of San d'Oria in Final Fantasy XI ends with this trope. With Prince Trion aiding your party in the fight, the head of the Orcish tribes, Warlord Rojgnoj, falls at your feet. In the FFXI universe, the orcs are beastmen who patrol various regions of the game, attacking adventurers at will - their reasoning for this? The very sword that Trion wields, one with enough power to separate a peninsula from the mainland and driving the inhabitants of a former powerful city underground. Rojgnoj tells all of this to us in broken English (or Japanese or French, depending on where you're playing from) and tells us this was the cause for the orcs waging war against the Kingdom of San d'Oria 20 years ago. It caused him and his people pain, and they simply wanted to destroy it. He dies shortly afterward.
Cliff Hudson from the first Dead Rising is also an example. A Vietnam war veteran who is experiencing war flashbacks due to the death of his granddaughter at the hands of zombies, and has become psychopathic as a result. When in his death throes, he snaps out of his madness, resulting in an extremely sad death scene. He is one of the few Psychopaths that most players regret killing.
The two major antagonists of Golden Sun: The Lost Age, Karst and Agatio, die of hypothermia in Mars Lighthouse after being turned into dragons and forced to fight the heroes until they're too exhausted and injured to warm themselves or escape. Agatio, The Generic Guy to the end, just tells the heroes to continue their mission and fire the Lighthouse for them. Karst, on the other hand, received just enough Character Development to shed sympathy on her Roaring Rampage of Revenge, so when she begs Felix to comfort her, it's both surprisingly moe for her and a flat-out Tear Jerker for us. Needless to say, a lot of fans rescue her in Fan Fiction.
In Devil May Cry, after you defeat the recurring Worthy Opponent Nelo Angelo, it's revealed that he was really Dante's twin brother Vergil. Vergil also qualifies for this in the third game, when he chooses to stay in the demon world after losing to Dante.
In the Dynasty Warriors series, Cao Cao was always portrayed as somewhat villainous and cruel. However, in the seventh game, it showed that beneath the coldness, he does care about the people who serve him, and he does wish for the chaos to end. Right before his death, he pleads for Xiahou Yuan and Dian Wei (both of whom died serving their lord) for their forgiveness.
The Nazis at the end of The Saboteur. As you approach their hideout in the Eiffel tower, you first assume that one of them has accidently fallen—you hear him scream and see him splat in front of you. Then, several of his comrades follow suit. The lobby is filled with dead, dying, or sobbing Nazis, one of whom drags himself towards you on his belly, choking out that, "He-he's killing everyone!" One of the soldiers plays a slow and mournful version of the game's theme, 'Feeling good', on the piano. To get to the elevator, you pass by a cluster of Nazis who hanged themselves, and at least two are play a tearful game of Russian Roulette with their pistols. Approach them, and Sean will murmur, "Keep at it mate—you'll get it right soon enough." Brrrr....
In The Legend of Spyro: Dawn Of The Dragon, it's revealed that the Apes were given a Fate Worse Than Death by Malefor so terrible, it's rather hard not to feel some sympathy for them. They were turned into living skeletons, forever cursed to remain in the shadows and feed off the energy of others, unable to ever be full. Even Spyro and Cynder are visibly horrified by this.
Thorne in TRON 2.0. Yes, he was greedy and made an exceedingly stupid mistake (that laser caused his wife to die, and his best friend to vanish - Alan Bradley is not kidding about the safety protocols!). But his PDA testifies to a lonely, frustrated life (the contact list comprises work contacts, his mother, and a shrink), and he dies horribly (being eaten alive by The Corruption).
The Carpenter in Alice: Madness Returns, all of his actions involving sinking ships and building an underwater town were to protect his part of Wonderland from the Infernal Train. Said train smashes its way through the Carpenter's theatre, and he moves himself into its path so it doesn't hit Alice.
Revas: You know what? It doesn't fucking matter anyway. [Looks down the shaft with an expression of fear] Just don't forget me... [Lets go]
At the end of Batman: Arkham City, he's been around two games while kicking dogs and generally doing his best to piss you off. However, the death scene of The Joker is surprisingly sad, even when you know he had it coming.
Batman: Do you want to know something funny? Even after everything you've done... I would have saved you. Joker: (By now laughing and coughing uncontrollably) That actually is... pretty funny...
Portal 2 has GLaDOS and, arguably, Wheatley. Neither of them die, but during the core transfer, GLaDOS screams in pain and it's terrifying. Wheatley shoots right into antagonist territory, destroying her power. And then you transfer them again, and throw him into space, and he gets an absolutely heartbreaking apology monologue. It makes you wonder who to feel sorry for at that point.
The guy's long-dead when you first hear him, but Cave Johnson. Specifically, when you hear his recordings from the 1980s, and his company's nearly bankrupt and he's dying of moonrock poisoning.
The Great Wolf Sif in Dark Souls. He can't really even be called a villain — Sif is just having a knee-jerk reaction to someone trespassing near his friend's grave. Near the end of the battle, Sif even starts limping in pain as he valiantly struggles to protect Artorias' grave from an Undead monster (i.e., you). Sadly there's no way to spare him since you need Artorias' ring to proceed with your quest, and the only way to get the ring is by killing Sif.
Skies of Arcadia gives us Ramirez's death at the end of the game. When all that's left of him is his crystal, Vyse expresses sympathy for Ramirez and requests to give him an honorable sailor's burial. Notably, he's the only real villain in the game that's shown in a truly sympathetic light, and whose circumstances are seen as a tragedy.
Dragon Age II has two major examples: Meredith and Anders (if you choose to kill him). Both started out as reasonable people who were corrupted by a combination of supernatural forces and their own prejudice or anger and both have tearjerking death scenes: Anders tells your Player Character "I'm glad it was you" before s/he kills him, with a look of anguish and remorse both before and after being stabbed. Meredith turns herself to stone in the midst of her Villainous Breakdown, permanently frozen in a nightmarish expression of rage and fear.
Many of the possessed Mages faced in the game. After being backed into a corner by the Templars, they resort to Blood Magic out of sheer desperation and end up becoming monsters. Made even worse where in some cases, Hawke arrives only a few moments too late to be able to save them, such as with Ser Thrask's daughter.
The Arishok. He spent three years stuck in Kirkwall and was unable to leave until he found the Tome of Koslun, thus fulfilling his duty to the Qun. It's heavily implied that part of his motivation for invading was to either cleanse the city of it's corruption or die in the process, with his dual to the death with Hawke being an intentional Suicide by Cop.
Duvall, the main villain in Haze, is an extremely arrogant and over-confident jerk for the entirety of the game. When's he fatally wounded in the final duel, however, it's hard not to feel sorry for him when he's sobbing, and then begs you not to tell his mom what he's done (slicing off fingers, killing people, etc.).
Surprisingly enough, Geese Howard from Fatal Fury. At the end of Real Bout, he receives a Power Geyser from Terry, which sends him flying towards the window. As he is about to plunge to his death (again), Terry holds his arm to save him. Geese simply smiles and shrugs him off, falling to his death while laughing.
In Garou, we learn he left his son Rock for Terry to take care. Probably because Terry could be a much better father that he could ever dream to be.
The Stranger who abducts Clementine in Telltale's The Walking Dead game. Before that, he was just a father trying to keep his family alive through the Zombie Apocalypse, but after losing his son while they were hunting and having all his family's supplies stolen while they were searching for him, his wife and daughter took off on their own only for him to find them as Walkers the next day. And the ones who took his family's food were your group.
Pedro Montana, from killer7, is a total bastard who sells orphans so that their organs can be used for Heaven's Smiles. But when we actually see him, he's playing handball when his partner, Curtis Blackburn (whom Pedro recently betrayed and ran out on), arrives. Pedro is terrified when he sees Curtis, and soon we discover he had a damn good reason to be - Curtis doesn't forgive. In this case, Curtis's idea of proper retribution is slaughtering Pedro's entire family... and then taunting him with stories of how they died. It's one of the hardest scenes in the game to watch, and makes it very clear that, out of all the villains in the game, Curtis Blackburn is the worst.
While Paper Mario: Sticker Star is undoubtedly the Lightest And Softest game in the series, the fourth boss, Mizzter Blizzard, was revealed to have a tragic backstory that led to him getting the Royal Sticker, which let him live like he wanted to at the cost of his sanity. He regains his sanity after losing, at which point he reveals his backstory and that he got the Royal Sticker as a result of praying to have a body that wouldn't melt. He then, in a playful manner, asks Mario to rebuild him next winter so they could play again, this time on friendly terms. To drive it all home, the narration of his backstory, which is third person for all other bosses, is in the first person here.
Ulfric: I'll never surrender Skyrim into the hands of a corrupt and dying empire! Rikke: Skyrim doesn't belong to you, Ulfric. Ulfric:No...but I belong to her.
Radiant Historia has a Final Boss that goes down like this. The version of his death in the Golden Ending is the most moving. The world in Radiant Historia is constantly in danger of becoming a lifeless desert, and only the voluntary Human Sacrifice of a member of the royal family of Granorg can postpone it. When it was his turn, he refused to go through with it because he didn't see anything in the world that was worth saving, and spent the game trying to make sure the only other remaining potential Sacrifice - you, his nephew - doesn't become one either. When you defeat him and make it clear that you're going to go through with it whether he likes it or not, if you've achieved 100% Completion, he decides that you are something in the world worth that's worth dying for, and performs the Heroic Sacrifice himself in your place.
While most Templars earn sympathy for their earnest beliefs that they're making the world a better place, sympathy for the penultimate Templar target, Sibrand, is earned because of how pitiable he comes across at his death. Of all the Templars he took the knowledge of the Piece of Eden's existence the hardest. Believing the Apple was proof that God didn't exist and that there was no afterlife, Sibrand goes through a steady Villainous Breakdown brought on by paranoia that Altair would kill him just like he did to the rest of the Templars. By the time of his death, Sibrand is so crazy that he's firing at white birds because he's afraid they might be Assassins, and his final words display just how horrified he really is at the thought that he will no longer exist.
This actually happens so often in the first game, that one of the most notable assassination targets is an aversion of this trope. When Altair asks Majd Addin if, like the other Templars, he'll try to justify his crimes as being done for a greater good, Addin merely scoffs at him, saying that he murdered people for fun, because it made him feel like a god. Altair, who has been steadily becoming sympathetic towards his targets as the game's gone on, decides to show Addin exactly what happens to people who put themselves above others by shanking him in the neck.
While most of the Templars in Ezio's tale have turned from Well Intentioned Extremistsinto power-hungry murderers and schemers, at least some of his enemies still manage to be sympathetic, such as Dante Moro. Friend and bodyguard of Marco Barbarigo, Marco eventually decided that he wanted Dante's wife for himself, and put a hit on his "friend" in order to get her. While Dante survived, a stab wound delivered to the head resulted in him being brain damaged, which Marco exploited in order to get Dante to divorce his wife. As an easily malleable tool for the Templars, Dante falls to Ezio, but seems to gain some semblance of his old self in his last moments, helping Ezio by telling him where the remaining Templars have fled. His death delivers an additional punch when Ezio finds a letter written to Dante from his ex-wife where she expresses that she still loves him, has never given up on him and now, with Marco dead, she promises to help him get his mind back.
Girolamo Savonarola, a monk not affiliated with either the Templars or the Assassins, he gained possession of the Apple of Eden and used its power to take control of Florence. Being a Well-Intentioned Extremist trying to purge Florence of everything he viewed as evil, it's hard not to feel bad for him when he's defeated and nearly burned alive by an angry mob. Even Ezio pities him enough to deliver a Mercy Kill rather than let him die in such agony.
Haytham Kenway, the father of protagonist Connor, dies following a duel with his son. Having spent so much time futilely trying to convert Connor to the Templar side, he acknowledges, in his own way, that he's proud of his son for the admirable qualities he's displayed. Connor takes no satisfaction in his death, and it's quite a sad sight to see when Connor arrives at his funeral where Haytham's mourners are weeping and Charles Lee is delivering an impassioned eulogy on what a good man he was.
Charles Lee, despite being Connor's Archenemy and a cruel Smug Snake, also gets a sympathetic death. Unlike nearly every other assassination target, Lee has no final words. Instead, after his friends are dead, his plans are foiled, and he's been gravely wounded by Connor, Lee flees and eventually takes refuge at the Conestoga Inn. However, Connor manages to track him down. Faced with his imminent death, Lee reacts with dignity, wordlessly sharing a drink with his nemesis before giving a nod to Connor to let him know he's ready.
Benjamin Hornigold defected to the Templars because he wanted to make the world a better place after seeing Nassau devolve from the democratic society he and his friends first envisioned it would be into a Wretched Hive. Though treated with contempt by Edward for his betrayal, Hornigold still attempts to warn Edward about how lonely and empty his life will be if he keeps going down his selfish course. By the game's end Edward has made peace with his deceased friend, as he imagines Hornigold sitting at a table drinking with the rest of their friends they lost along the way.
Bartholomew Roberts, the merciless, Wild Card pirate not aligned with the Templars or the Assassins, faces his death with dignity, always knowing that his life would be a short one but a merry one. The only regret he has is that he was Born in the Wrong Century and that, because of this, this incarnation of him would never be reunited with his one true love, Juno. Just before dying he asks Edward to dispose of his body, knowing that the Templars would use it to control the Observatory for themselves.
Beatrice falls in this trope. She starts the series as a witch who loves to kill Battler's family in the most horrifying ways, but in EP5 it's confirmed that she didn't actually enjoy doing this, and in EP7 we are shown just how Beatrice came to be. After she's broken, Bernkastel keeps playing with her.
Acro's defeat as well, with his remark (that you have to interpret for Regina) about how he wanted to stick around. He's worried that he might be in prison or executed by the time his brother gets out of his coma.
Caster in Fate/stay night's "Unlimited Blade Works" scenario. Yes, she captures and tortures Saber, holds Taiga hostage, and is responsible for many a Bad End in Unlimited Blade Works, including one where she orders Shiro's friend, Issei, to kill him. Yet her last moments were so touching, it almost made you forget all that.
Kirei Kotomine in Heaven's Feel, even more so. His actions in the route, and the backstory it reveals, does an impressive job of building sympathy for him, considering that he lives to see others suffer and is actively trying to destroy the world. Seeking the reason for his twisted existence, he died without regret. No wonder Shirou realized that he liked Kirei.
Zouken Matou. It's difficult to feel sympathy for the monster he's become, but you might just pity the idealistic Zouken Makiri, who kept seeking immortality so that the woman he loved wouldn't have died in vain.
Ilya, who in 'Fate' was a psychopathic monster at worst, appeared in 'Unlimited Blade Works' long enough for a tearjerking finale with backstory that managed to woobify her without even giving away her whole Freudian Excuse (which was saved for 'Heaven's Feel'). And Berserker, already Deader Than Dead from his Self Destructive Charge, managed to stand long enough to give her comfort before both died.
In strip 830, it's really hard not to pity Tsukiko — an unrepentant Card-Carrying Villain who sold out her own city to Xykon — when Redcloak usurps control over her wights, who she'd treated like her own children, to prove that undead are little more then automatons for necromancers of any stripe. And then he has them drain her to death. And then eat her. She was a sick, twisted, self-confessed necrophiliac who was obsessed with Xykon because every living person she ever met in her entire life treated her like crap. What puts her solidly in Alas Poor Villain territory is that she really and truly loved him, and only died because she discovered concrete proof that Redcloak is manipulating Xykon, and that the MacGuffin they're after won't get Xykon the power he wants. The point really gets hammered home when the only person to mourn is the Monster in the Darkness, who points out that in the end, Tsukiko just wanted to be loved.
Demon-roach: So what? Who cares? MitD: Exactly. That's why I'm sad.
Nale's death in 913: Independent has caused some of these reactions. Nale is a petty, selfish mass-murderer, but hearing his anger about being treated like a tool by his father, and refusing his father's help to his face shows that he has balls, only to get stabbed by his own father. Plus Elan's reaction...
Vriska Serket, who had spent the entirety of Act 5 Act 2 getting closer to John and finally admitting that she wanted to try living a normal life. She was killed by Terezi in order to prevent her from fighting Jack, which in an alternate timeline got everybody except Vriska and Aradia killed. Her final message? Telling John that if and when they finally do meet, she'd like to go on a date.
Courtyard Droll, Jack's clueless underling who fails at being evil, which gets his superiors pretty annoyed with him. When he finally manages to follow one of Jack's orders to the letter (Jack had ordered him to kill Jade, something Jack himself couldn't do due to his Undying Loyalty from Bec's prototyping), Jack snaps and kills him.
Tobun in Penny Arcade's Cardboard Tube Samurai storyline, is implied to have become a Death Seeker after being compelled to commit atrocities. Fighting the CTS hand to hand, his last words are "before this moment, did I ever see the world?"
Mega 64 Version 3 ends with the legitimately tragic death of Dr. Poque, who started the series as the main antagonist.
In the Global Guardians PBEM Universe, the villain Hardcase was generally thought of as a brutish, selfish thug who liked to beat up women for fun, drank too much, and was generally a sleaze. And on September 11, 2001, he gave his life by using his superhuman strength to save people from the collapsing North Tower of the World Trade Center. The heroes not only campaigned to get him a posthumous presidential pardon, they sprang for a funeral the likes of which are normally reserved for deceased presidents and popes.
CT in Red vs. Blue (no, not the one from Season 7, the real Freelancer who the Rebel Leader took the identity of) was never really a villain in the first place, but instead ended up becoming a Hero Antagonist to try and take down the Director. Her reward for trying to do the right thing? A throwing axe to the chest which mortally wounds her, causing her to die in her lover's arms.
The Director also got a moment like this in the finale of Season 10, when he realised he should have spent more time looking after his daughter Carolina, realises that he has been chasing at ghosts futilely for several years, asks Carolina for a pistol, makes peace with her and F.I.L.L.S and then is implied to commit suicide.
Scion of Worm was unquestionably a sadistic, Omnicidal Maniac, but the way that Taylor defeated him by taunting him with the death of his counterpart makes it hard not to pity him.
In Beast Machines, Rhinox, a former ally, has become Tankor, a powerful enemy. After Tankor's death, the heroes hold a memorial for their fallen friend.
Cheetor: He wasn't just one of us... He was the best of us.
In nearly every Mr. Freeze appearance (except the one where he finally gets a happy ending and the one from The New Batman Adventures), he is defeated in a tragic and Tear Jerky way, culminating in this final exchange in his last appearance (both in Real Life and in the Universe timeline), where he lets himself be caught in a collapsing building.
Batman (Terry): Freeze, you have to get out of here! The whole place is coming down! Freeze: Believe me... you're the only one who cares.
Solomon Grundy in a single episode (or rather two connected ones), goes from regular villain to sympathetic villain, who dies in his quest to attain his lost soul. For good measure, he's brought back again in a later episode, this time truly soulless, and has to be put down Old Yeller style.
Grundy: Do you think... Grundy's soul is waiting for him? Hawkgirl (A confirmed atheist): Grundy, I don't belie- (stops herself) Yes. It's waiting for you. Grundy: Then Grundy... gets his reward.
Though she doesn't actually die there, Demona's defeat at the end of "City of Stone" certainly counts, as a broken Demona, for a brief moment, realizes and regrets the evil she's done over her thousand-year life, and then gives the heroes the password they need to shut down her scheme. It doesn't hold, but for a moment, you stop hating her and just feel sorry for her.
Demona: The access code is... 'alone'.
There's also the Captain, who was so wracked with guilt that he spent the next thousand years haunting the castle's remains after his death. Hakon was also haunting the site, but out of continued hate for Goliath (who ironically had nothing to do with either of their death's who killed each other Disney style, although he wanted to deliver a gruesome kill). When Goliath shows up at the castle again, they harass him, make him hallucinate and attack his own friends, and, finally, drive him to an ancient ritual site where they can exchange his life for theirs. The Captain realizes what evil he is about to commit, repents, and uses his brief physical form to destroy the site. With his last moments, he thanks Goliath for forcing him to acknowledge his sins and begs for forgiveness as he travels to the afterlife. This is such a Crowning Moment of Awesome that Goliath happily mourns him as a friend who is finally at peace. Hakon is still stuck, trapped within the ruined site, alone to wallow in his hate.
General Shiva in Exo Squad; imprisoned for not slaughtering the Australian Resistance to the last man, he is given a chance to "redeem himself" by retaking Venus, which he knows to be a suicide mission. But, being a good soldier, he gives it a go anyways. When he gets shot down, even the Exoscouts who find him see it as a tragedy.
While he has a number of fans who sympathize with him, Vlad Masters in Danny Phantom remains the overall Big Bad and performs his share of Moral Event Horizon acts. Still, his final moments gave him a big woobie moment when he not only had to deal with the fact that everyone he wanted would not give him their love, but his most hated "friend" of all people rejected him when he refused to change his evil ways. Now, Vlad doesn't have anyone and is stuck in an area where he has to confront his greatest fear: loneliness.
Hun in Turtles Forever, after the Turtles finally convince him that The Shredder is going to destroy The Multiverse. Hun is erased from reality right afterwards. The same thing happened to Casey and April, and we see them both get better once reality is restored, so we can assume Hun was brought back too.
Leonardo: You heard the man. Let's go stop the Shredder.
The Decepticons got some of their members killed unceremoniously in Transformers Prime. Breakdown was eviscerated by Airachnid. And Dreadwing, who wanted to kill Starscream who zombified his brother Skyquake, was killed by Megatron for disobeying his order to stand down.
Additionally, several MECH members end up being killed by Silas as he views them as useless now he is a human-Transformer hybrid, just after they saved him of all things. It's pretty hard not to feel sorry for them in this case.
TRON: Uprising: Keller's a scientist forcibly drafted into the occupation to force them to mind control other programs. She chafes, and helps the Renegade stop her concoction before going on the run, with the Occupation force chasing after her. She spends an entire episode in a state of panic, trying all manner of options to desperately escape while trapped on a train, nearly dying at least twice, and Beck, sympathetic to her position, trying to recruit her. At the very end, cornered, she goes back to the Occupation with Paige promising her no harm, but not before covering for Beck so no one knows he's a Resistance sympathizer. She goes to back to the general, who welcomes her back, and kills her like every other minion who displeases him.
Major Jakov. The sheer brutality with which Barry usurps and then murders him makes his death a genuine Tear Jerker, both for the audience and In-Universe.
If he even counted as a villain, then Captain Murphy-he wasn't even a bad guy, just a harmless, if unstable, guy who went nuts and started making terrorist threats due to being trapped at the bottom of the ocean, but Archer's idiocy gets him killed, and he tells them how to escape the lab with his dying breath.