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 then on made plans and took actions that caused the deaths of hundreds of thousands, all while taking a sadistic pleasure from it in 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, after Frieza shoots him for describing Goku as a Super-Saiyan, we get Vegeta's lengthy final speech about his genuinely horrendous childhood, and see Vegeta crying as he begs Goku to kill Frieza and avenge their people, before breathing his last in a Big Sleep from his terrible injuries.
Zangya may have been ruthless, but still, seeing her in her last seconds of life betrayed and mercilessly murdered by her own leader Bojack, a lot of fans feel sorry for her, though this could be attributed to Draco in Leather Pants.
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. Even then Goku is visibly shaken and reeling after having to kill Frieza, although more out of pitying Frieza's self-destructive foolishness than any sympathy for the bastard.
Vegeta gets another moment like this during the Buu Saga. After deliberately becoming one of Babidi's Majins to become stronger, killing scores of innocent people to provoke Goku into fighting him, and causing Majin Buu to be revived by his actions, Vegeta ultimately realizes what a selfish dick he's been and how badly he screwed up. When he asks Piccolo if he will be able to see Goku in the afterlife, Piccolo tells Vegeta point-blank that he'll most likely be condemned to Hell for his past crimes. Vegeta sacrifices himself in an attempt to kill Buu regardless, fighting for someone other than himself for the first time in his life.
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. Although considering everything she did you him, one has to wonder why he didn't just let her die.
K: Return of Kings has the Green and Grey Kings. As Shiro enacts his plan to destroy the Slates, Nagare, the Green King, asks why Shiro rejects his Well-Intentioned Extremist plan to give the whole world superpowers. Shiro and Neko tell him that they don't need any of that - just warm food and friends to share it with around a small table. Nagare thinks back to his Clan's secret base, which was a lot like that, and remembers their warm life together as he dies. Then, the Grey King, who was like a father to Nagare, comes and holds Nagare as they die together. Afterwards, their remaining Clansmen toss flowers into the spot where they died and remember them.
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.
Caster and Souichirou's deaths in the Unlimited Blade Works route Fate/stay night were definitely this. Caster is killed by Archer (an entity who is much stronger than her) while trying to protect Souichirou, her lover. When Caster is killed, Archer gives Souichirou the opportunity to flee for his life but Souichirou is so upset at her sacrifice he tries to avenge her death, and is effortlessly killed by Archer. Even our protagonists are upset at their deaths.
Illya's death in UBW (killed by Gilgamesh) is also very sad. Illya might be a homicidal woman-child but the brutality at which Gilgamesh kills her is unnecessarily harsh, especially considering Gil didn't even need to kill her.
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.
Madara of all people. For all his power and arrogance, he's ultimately the biggest loser of them all, as his plans end with his death while Hashirama's "Will of Fire" endured and will continue to endure long after he [Hashirama] passed on. The only comfort he has is that in spite of everything that transpired between them, Hashirama (briefly revived by the Edo Tensei), perhaps the only person to have ever truly empathize with him besides his brother Izuna, still considers them friends.
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 (probably because they never die, and if they show up again have completely recovered). The other end has some more sympathetic villains, such as...
Mohmoo. Poor, poor 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 little more than The Chew Toy for the Straw Hats…and he's seen almost perpetually crying because of it.
Oda's SBS also makes Magellan this; the picture we see of him as a child shows him attempting to water some flowers, and crying when they die due to the poison oozing off of him.
Senor Pink from the Dressrosa arc. At the time of his defeat, his past is revealed: the woman he fell in love with was in a permanent catatonic state, and his son by her died as an infant. As he loses consciousness, he reflects on how much he wants to see them again.
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 desperately, grovelling in panic. The manga's epilogue chapter ends with a large procession, holding a candle-lit vigil for their dead "savior". The anime even flashes back briefly to when Light was just an Ordinary High-School Student to drive the point home.
Nephrite too. He genuinely begins to love Naru immediately prior to his getting killed by Zoisite's demons, and among his last words is that he asks Naru to forgive him that they never got to eat chocolate parfaits together. Sailors Moon, Mercury and Mars are all visibly sobbing along with Naru when Nephrite breathes his last and disappears in a cloud of sparkles.
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. Prince Diamande even sees her crying out to him 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 resurrection.
Also, Viluy was a bit of an Alpha Bitch, but her death was so utterly cruel that one has to have pity for her. Even Ami expresses pity upon witnessing it.
"She only believed in machines... So sad"
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 (Iron Mouse, Aluminium Siren), calling out to loved ones (Red Crow), or still half-possessed by Galaxia and incapable of taking action (Tin Nyanko). 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.
Master Asia from G Gundam. First, he congratulates Domon on his victory. Second, as the Master Gundam expodes, Domon remembers all of the good times he had with Master Asia. Third, the ghosts of the Shuffle Alliance apologize to the dying Master Asia for not realizing how great his despair at the Gundam Fight was. Fourth, Master Asia aplolgoizes to Domon for everything he has done and the two of them recite the motto of the School of the Undefeated of the East before he dies peacefully.
Treize Khushrenada from Mobile Suit Gundam Wing allows Wufei to kill him to atone for everyone who has died for his war.
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 too, 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 dub version is even more sympathetic: "If this is how it must be... protect the universe at all cost."
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 Harribel and Starrk. With Harribel and Starrk, 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 Stark's Death and Harribel's defeat that she (barely) lived through were a pointless waste orchestrated by a man who couldn't care less about them. Here, however, 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.
Nnoitra's very regretful glance at Nelliel as he falls to his knees just cements it.
Wonderweiss Margela. Captain-Commander Yamamoto-Genryusai, 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.
Baraggan Louisenbairn, probably the most arrogant Espada, who destroyed Sui-Feng's arm (she got better), lost his position as the King of Hueco Mundo by Aizen years ago, and he was forced to serve for him as the Segunda Espada. Baraggan wanted to get his throne back, and when he was dying, he throws Gran Caida to take Aizen with him to death, but the axe vanished before it could reach Aizen because Baraggan died too early. Everyone on the battlefield, whether comrades or foes, were shocked about this event. Everyone but Aizen, who didn't even look at him.
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.
However, Aizen is still alive and in prison.
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 Yhwach, but before Yhwach 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.
Invoked by Lelouch's death, one of the saddest scenes in the series, which was a bit of an All According to Plan.
Mao's death as well. He was just an orphan driven insane by a case of Power Incontinence who couldn't deal with the world on his own.
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.
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 piece. 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.
Gaelio Bauduin from Mobile Suit Gundam: Iron-Blooded Orphans is a cheerful Gjallarhorn officer who believes in justice, he doesn't do anything villainous in his entire life, and in fact wants to reform the organisation from the inside. The only thing makes him a villain is the fact his job is to stop the protagonists. Not only he has to see his friends getting maimed and killed by Mikazuki, his gradual breakdown has corrupted him into a sad and vengeful person. And in the end, he dies with the knowledge that his friends were betrayed by none other than his childhood friend, and the said friend would marry his 9-year-old sister.
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 Future Diary, 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.
The Egg of the Perfect World is one of the few villains in Berserk that is actually LIKABLE. His death scene, where he selflessly sacrifices himself for Griffith, is very heart shattering.
Z-one in Yu-Gi-Oh! 5D's. 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.
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 is a teenaged 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. The last time he's seen, Souma is sobbing and holding his brother's lifeless body in his arms as the snow falls on them...
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.
Annie Leonhart, from Attack on Titan. As the Female Titan, she spends an entire story arc terrorizing and slaughtering the members of the Survey Corps while on the hunt for Living MacGuffin Eren. She kills many of her victims in brutal and unnecessarily cruel ways, including spinning one poor soul by his grappling hook wires until his body folds in half backwards. Once she's finished making a fine paste of Red Shirts, she systematically kills each and every one of Eren's new comrades from the Special Operations Squad right in front of him before beating him soundly and kidnapping him. Though she fails to escape with Eren, her attack leaves many dead, Levi badly wounded, and the mission failed so miserably that the future of the Survey Corps and Eren looks doubtful. But when she's finally exposed and defeated, we're treated to multiple flashbacks to her beloved father training her to fight. In desperation, she tries to Wall Crawl up Wall Sina to escape and is knocked from the Wall by Mikasa, quickly subdued by Eren and the military. She recalls her father on his knees before her, crying as he admits that he was wrong. He tells her to consider the entire world her enemy, telling her that he's the only one who is on her side, and makes her promise to come home to him someday — weeping, she encases herself in a Crystal Prison to prevent her capture.
As Kenny Ackerman lays dying, he flashes back to his life, from meeting the previous owner of the King's power up to it being passed on to Frieda. He's shown to have genuinely befriended and respected Uri, and as he dies, he tells Levi that everyone, including Uri, Levi and himself were drunk on something and enslaved to it, whether it be alcohol, power, religion, etc. His final words in response to Levi asking why he abandoned him:
I...was...unfit...to be a parent.
The death from Helbram from The Seven Deadly Sins is portrayed rather sympathetically. After at least 700 years of being driven mad with hatred for humans due to what happened to him, his friend King finally fulfills their old promise and puts Helbram out of his misery for having cross the Moral Event Horizon. Having been given the fatal wound, Helbram returns to his former innocent psyche and dies grateful for what King has done for him.
Another example is the Big Bad of Part 5, Diavolo. He spends a good deal of the arc trying to kill his daughter, but he meets his end at the hands of the godlike Gold Experience Requiem, which forces him to live out an infinite cycle of deaths. The fact that he's running away from a girl not long after kind of drives this home.
Cobra's thoughts: "My prayer...I...just wanted to hear the voice of my one friend...Cuberos..."
In Senki Zesshou Symphogear GX, while Maria, Kirika and Shirabe aren't exactly shedding tears over Dr. Ver's body, they do at least seem saddened by his death in Episode 12 of GX.
Dragon Ball Kai: Astoundingly, Ryusei Nakao manages to make Frieza's suffering, as he laid dismembered and begging for Goku's help, invoke the pity and sorrow that the latter felt from the audience this time around. Living and breathing the character for over twenty years helped him bring a genuinely pathetic vulnerability and sincere "humanity" to his performance. Kenji Yamamoto's decision to use a cello score during the recut made the scene a borderline Tear Jerker (when the score was replaced, the recycled music from DBZ worked well too, but not quite the same way as Yamamoto's).
In Ravages Of Time every single dead villain receives at least a chapter as a eulogy, making Yuan Shu and Lu Bu look extremely sympathetic.
Nutcracker was a Dominatrix that earned her nickname from her signature Groin Attack, and was part of a human trafficking ring. In her final moments, we're shown glimpses of her past — a filthy little girl looking at the models on display in a store window, and the same little girl repeating a mantra of needing money while surrounded by a group of male figures that leer down at her. Her final words are that she just wanted to be "pretty".
Hairu Ihei is introduced as a Cute But Psycho Investigator and takes considerable pleasure in killing. She comes across as petty, childish, and utterly vicious without an ounce of morals. Then, in her final moments, she recalls her childhood at a Tyke Bomb factory and the happiness she got from Arima paying attention to her.
Kanae von Rosewald is a reoccurring villain, slowly being consumed by his jealousy and hatred of Sasaki. But his focal chapters establish him as an orphaned girl that adopted a male identity to carry on her family's legacy and sacrificed her own happiness in service of Family. When Tsukiyama is thrown from a high-rise building, Kanae leaps after him and makes a Dying Declaration of Love before sacrificing himself.
"The sorrows of life — to not be able to live like yourself. The joys of life — to be able to die like yourself. Do I deserve to be this happy?"
In Shikipretty much every villainous character can fall under this one way or the other, especially considering several of them weren't really evil at all, doing things either out of ignorance or necessity.
In Endride, Prince Emilio may have spent much of his life wanting nothing more than revenge on his Parental Substitute King Delzaine (who reportedly killed his father and is shown to be an unsympathetic ruler), but when Delzaine dies protecting him from Ibelda, Emilio regrets it heavily and it's not hard to feel sympathetic. There's also an element of this when Ibelda needlessly slaughters his fellow Truculent without warning.