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 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....
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.
In the Sin City album Hell and Back, Wallace feels some pity after he kills Deliah, the contract killer who tried to seduce and kill him, calling her a "strange, sad creature" before silently closing her eyes.
The Crime Master in the end of Agent Venom's first volume. Not only does he get shot dead by his own sister but his last words, rather than swearing vengeance or cursing his enemies, are just this:
Toxin gets a similar reaction from Venom mainly because he was forced into the role and died before Venom could save him.
When the first Porcupine (Alex Gentry) died helping take down the Serpent Society, Captain America was deeply saddened by his old foe's demise and even insisted on giving him a memorial in the Avengers Mansion, a right usually reserved for longtime Avengers and worldchanging heroes. Given that Porcupine was a Friendly Enemy to Cap at best and an Ineffectual Sympathetic Villain at worst this isn't terribly surprising.
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 he 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.
Hivefled: Dualscar was a slave-taking Jerk Ass who tried to have his ex murdered, but it's hard to imagine he did anything that would make him deserve the death he got.
Young Justice Darkness Falls: Volcanna in this fic was a lustful fire wielding fury who caused nothing but trouble for the league and team, and had a rather unsettling obsession with Superboy. However, her dying for her comrade Big Barda when they decide to desert the furies was a surprisingly touching moment, and her death was treated not with contempt but with sympathy.
In the My Little Pony/Dresden Files crossover The Dresden Fillies False Masks, the entire Order Triune becomes this. They are sacrificed to a demon by Novel Notion. Considering they spent the whole story trying to kill Harry thinking he was someone who had been dead for 1200 years, endangered many lives, and betrayed the very kingdom they swore to protect, it is karmic. But it becomes tragic when you realize that they had been misled this entire time, they genuinely wanted to protect Equestria, and had been betrayed by one of their own. The way they go is also terrifying: running for their lives as the circle swallows them, with the pegasi who tried to fly away being swat down like flies. Afterwards, all that's left of them is some blood. The horrified reactions of the Mane 6, and even Harry seal this.
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, there is a 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. 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.
Wreck-It Ralph: King Candy/Turbo's death. Granted he is an evil selfish asshole that only cares about himself but watching him fly into the coke volcano panicking while an epic farewell version of his theme plays in the background might get you to have a little sympathy for this Disney villain.
In the 2014 Godzilla film, it's hard not to feel a bit sorry for the Mutos when the mother is mourning the death of her babies, especially when we see them meet and the father feeds a nuke to the mother and they nuzzle a bit before making the nest. The mother's anguished vocalizations manage to convey the message perfectly.
Gollum from The Lord of the Rings. The series frequently shows Gollum's sympathetic side. His death is played for tragedy as he finally gets his greatest desire, only to be destroyed by the attempt.
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.
Senator Kelly goes through absolute hell in X-Men and renounces his anti-mutant beliefs before dying.
In X2: X-Men United, halfway through her death scene, the mind-control serum wears off and Deathstrike is allowed a few tragic seconds of clarity to realize where she is and what's happened to her; the look on her face says it all.
Shinzon from Star Trek: Nemesis. While not the best Trek villain, there's no denying that Shinzon's life sucked. He was created solely 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.
Ironically subverted in Hitchcock's Strangers on a Train. Magnificent 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 the rancor's keeper bursts into tears and has to be led away.
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..."
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 in the American version of The Ring, 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.
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 II, 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 …"
In Alien: Resurrection, for all the murderous havoc the Newborn and it's entire race caused for Ripley, she's visibly sorrowful about having to kill it (and in an indirectly torturous manner at that).
Willie Lopez and Carl Bruner in Ghost. The scenes of them being literally dragged into the netherworld (not to mention what is probably 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.
Subverted in Scream 3 with the movie's Ghostface Roman Bridger. While Ghostface is dying, Sidney holds his hand because he's her lost brother. Barely a minute later he gets up to kill them all again just when they were sure he wasn't superhuman. Slasher Movie psycho killers have to be shot in the head to put them down.
Dr. Elsa Schneider in Indiana Jones and the Last Crusade. Indiana attempts to save Elsa when she causes a Cataclysm Climax by trying to steal the Holy Grail. He manages to grab her before she falls into a pit; however, her obsession with the grail leads her to reach wildly for it. Indiana tries to hold on, but her hand slips from its glove and she falls to her death. After escaping the temple, Indiana looks back with an expression of regret that he couldn’t save her life. His father shows less sympathy when he says, "Elsa didn't believe in the grail. She thought she'd found a prize."
General Zod in Man of Steel. After losing everything he had due to his refusal to coexist with humanity, he soars across the Despair Event Horizon and commits Suicide By Superman by forcing Superman into a situation where he has no choice but to kill Zod. After his death Superman breaks down out of remorse, having clearly wanted to find a peaceful solution.
Andrew from Chronicle. Being subjected to his Drunk Father's constant abuse everyday, his neglectful cousin Matt paying little attention to him until it's too late to save him, constantly being bullied by everyone in his school, once he gets telekinetic superpowers you can only imagine what's on his mind. Needless to say, when the time comes for Matt to put him down before Andrew could destroy Seattle, he was extremely reluctant to do so.
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?
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 while trying to be the mole.
The same could be said for Asharak, a high-ranking servant of Torak and manipulative bastard who messed with Garion for years, 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 it comes 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.
Warrior Cats has a tendency to do this with most of its villains, due to its Grey and Gray Morality policy. 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.
Cao Cao gets a long poem on his death, daring anyone to criticize him.
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 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.
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.
The Mortal Instruments — Sebastian Morgenstern goes down quickly, but Jonathan, the good within him, arises, tells Clary how to destroy the Infernal Cup, talks about what might have been, and then dies.
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 poignant 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 you 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 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.
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.
The Lord of the Rings: 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.
The 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).
Even before their deaths, most of the fates of the villains invoke this trope. Thanks to his mother forcing him into a fate he never wanted Tiberius goes from being a stern but good general and loving, loyal brother to being a depraved, paranoid loner manipulated by Sejanus and filled with hatred for Rome and his own family. Livia becomes a lonely woman deprived of most of the political power she once enjoyed (and actually used well), having to live isolated with the memory that she murdered a man she genuinely loved, with the fact that her faith in her son, whose rise to the imperial office she dedicated herself completely toward, was tragically misplaced, and finally with her own terror of being punished eternally in the afterlife. Caligula devolves from an eccentric libertine to a madman who is cursed with the occasional moment of lucidity and in his delusions of godhood tortures and kills his sister Drusilla, the one woman he loved (while she's pregnant, no less). Sejanus is reluctantly pushed into abandoning his lover Livilla by his political ambitions, which despite his ruthlessness clearly hurts him and pushes Livilla even further over the edge. Messalina may be an exception, and even she obviously becomes increasingly unstable and unable to comprehend the risks she takes.
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.
Flint from Requiem For Methuselah, was not totally a villain but he has become somewhat misanthropic after 6000 years of life. To his credit, he was once Solomon, Alexander, Lazarus, Leonardo, Merlin, and Brahms. He has met Moses, Socrates, Jesus, and Shakespeare. He used Kirk's obvious attraction for Rayna in the hope that Rayna (an android he created) would transfer the resulting feelings she experienced to him. This failed miserably and she was torn between her love for the young, handsome captain, and her love for the kind old man Flint whom she considered like a father. This lead to her eventual death by short circuit. Throughout the encounter, Flint interfered with the Enterprise's mission to aquire a much needed cure for a plague, threatened the Enterprise crew, and tried to take them hostage. In retrospect, Kirk, emphasized with Flint who, while having shunned humankind, only wanted the company of someone who was his intellectual equal, even if he had to build her. Kirk, on the other hand, was far too easily attracted to Rayna and thus manipulated by Flint, which did say something about him as well. Kirk summed it up: "An old and lonely man...and a young and lonely man."
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.
The episode "Long in the Tooth" features Joe, a Professional Killer for the Miami Cartel who is gunned down by Raylan while trying to make a deal with him. He manages to have a fairly lengthy conversation with Raylan before bleeding out, and it serves to humanise him.
Mags Bennet, the Big Bad of season two lives long enough to watch everything she worked her life for crumble. Her hometown despising her, her criminal empire going up in smoke, her two favored sons dead, her remaining living son in police custody, and the surrogate daughter she truly loved only barely being talked down from killing Mags herself, Mags opts to kill herself by drinking her poisoned moonshine. Her last words, a sincere echo of what she said to the man she killed with that very same moonshine, show just how far she's fallen into despair.
Marijuana kingpin Rodney "Hot-Rod" Dunham in Season 5. Betrayed by Johnny Crowder, and held hostage by Jay & Roscoe, Hot-Rod breaks loose and kills one of their men, only to take a bullet in the process. He's found moments later by Raylan and his own Friendly Enemy Alex Miller, and chats with the two of them for a few moments as he bleeds out, reminiscing about the old days.
Danny Crowe of all people gets a send-off like this. While his death itself is meant to be Black Comedy, tripping and stabbing himself through the throat while trying to kill Raylan, the minutes before that, where he's mourning over the body of his dead dog, Chelsea, and tearfully recounting how he rescued him from a puppy mill, does a lot to humanize a man who had otherwise been a stupid, psychoticasshole.
Stargate Atlantis: Subverted in "The Prodigal" with Michael. His fight with John Sheppard on top of the Atlantis main tower concludes with Teyla (who's most personally connected to Michael) and John throwing him off it. Michael holds on to the ledge and screams at Teyla for mercy. By this point Michael had already commited galactic genocide, kidnapped and experimented on Teyla's people, mutated her husband into a monster, tried to harvest her baby at least twice, and tried to kill her and everyone in Atlantis out of petty spite. She kicks his hands and watches him fall to his death.
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.
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.
Pierrot doesn't want to die! Pierrot doesn't want to die!
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.
Umineko: When They Cry: 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 you 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. Thankfully the Scratch brings him back. Sort of.
Snowman is a Jerkass, but it's hard not to feel bad for her when the Doc Scratch-influenced Spades Slick shoots her dead at the end of Act 5, especially since she had just saved his life a few moments before.
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?"
At the grand finale of Errant Story, Ian just keepsrepeating "I just wanted to help." Despite a personal body count in the thousands, he's quite serious. However, it doesn't keep him from getting his brains blown out.
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.
Although a lot of the villains in Arby 'n' the Chief are usually downright over-the-top like Craig, or downright hateful like Adam, the series's final villain, Eugene Black is certainly an interesting case of this. As evident throughout the show's final season, he's a downright sadist who has no trouble letting his psychopathic or pedophile friends do as they wish to people online, as well as enjoys forcing hundreds of innocent people to replace their Xbox 360s after banning them with a hardware corrupting software over a period of 2 months, just for laughs. On the flipside though, he's also a failing student at his school (despite also being a bully too), is constantly abused by his Drunk (and sometimes neglectful) Father, and his sister (the only source of happiness in his life) is dying a slow and agonizing death of Leukemia. It's hard whether to feel sorry for him for how crappy his life is, or to hate him for how much of a bastard he is just to repress these feelings. To add insult to injury, this only get worse for him, and he's Driven to Suicide by the show's end.
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; they both get better once reality is restored, Hun was likely brought back too.
Leonardo: You heard the man. Let's go stop the Shredder.
The Decepticons got some of their members killed unceremoniously. 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.