In The Lion King II: Simba's Pride, Nuka, The Un-Favourite, 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.
Lord Shen. After a very miserable and empty life, he finally faces the warrior destined to defeat him, whose entire species he tried to destroy... and the warrior has found inner peace, and doesn't want revenge. He cannot grasp how that is, how he could be free of all that pain, and tries one last time to kill him... only to accidentally kill himself. But he accepts it gracefully, because death is the only peace he can find.
Also, the Boss Wolf. He follows Shen's orders without hesitation or mercy, but when Shen orders him to fire the cannon at the heroes, not caring that their own soldiers would be killed in the crossfire, Boss Wolf refuses. Enraged, Shen strikes Boss Wolf with his throwing knives and fires the cannon himself.
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 the manner of his demise is rather tragic and horrifying. 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.
Dinosaur: Kron wasn't exactly a villain (just very selfish and completely stubborn), but despite everything her brother had done, Neera is deeply saddened by Kron dying of his injuries from the final confrontation with the Carnotaur.
Wreck-It Ralph: King Candy/Turbo's death. While he is an evil and selfish asshole that only cares about himself, watching him fly into the coke volcano panicking while an epic farewell version of his theme plays in the background can be horrifying and even somewhat saddening.
The witch named Agatha PrenderghastUsed to Be a Sweet Kid who, like Norman, happened to have the ability to speak to the dead. She cursed the zombies in revenge for killing her only for being different. She became so obsessed with making the townspeople pay for what they did to her that she completely forgot about the people who loved her and she almost completely lost herself in her rage. When she is finally able to find peace with the help of Norman, Agatha Disappears into Light to move on to the afterlife upon realizing that the only thing she really wanted was to see her mother again after the townspeople separate them.
The Judge (as well as the other zombies) have come to regret their actions over the hundreds of years they've been dead. When Aggie is finally at rest, they Disappear into Light to move on to the afterlife as they look scared and regretful.
King Kong (1933) and all of its adaptations give sympathy to the ape once he's dead with the final line, "Twas beauty that killed the beast."
Pirates of the Caribbean: At World's End gives us one for the Kraken, whose massive corpse stranded on a beach gets Captains Sparrow and Barbossa (both back from the dead) musing sadly about the end of an era it symbolizes, as well as for its master Davy Jones, stabbed through the heart and brokenly whispering the name of his lost love before he falls over the side of his ship and disappears into the maelstrom below.
Even if he is sadistic and self-serving, the downfall and eventual death of Norman Osborn/Green Goblin from Spider-Man is at the very least portrayed somberly. He even accepts his fate, but not before making a final request to Peter Parker/Spider-Man.
Dr. Octopus has a similarly tragic demise in Spider-Man 2. He never wanted to be evil to begin with, but his tentacles took the better of him. He even shows an epic defiance of his evil ways before choosing to drown with the fusion reactor to save New York from meltdown.
In Godzilla vs. Destoroyah, it's played again, this time far more successfully, with even several human characters who had dedicated their lives to beating Godzilla openly weeping at his demise. By now, he's a bit of an Anti-Hero, though.
The oft-maligned 1998 American version also has a strong influence of this at the end, for both Godzilla/Zilla himself AND his babies, and the scene where he nudges one of his dead babies in a futile attempt to wake it up is very sad. Then, at the end, after he himself is dying from his missile wounds on the Brooklyn Bridge, even after all the people who have died in the destruction that he caused, you can't help but feel a little pity for the big guy as he stares at Nick with a resigned look in his eyes. Then he closes his eyes for the last time, and passes away.
It goes all the way back to the original 1954 film; it's quite difficult to watch the beast in such pain as all the skin and flesh is ripped off his body, especially since the film shows that Godzilla is a Tragic Villain, and is as much a victim of the atomic bomb as everyone else. It makes his death at the end all the more heartbreaking.
In the 2014 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.
More of an "Alas Poor Mook" but in Jurassic Park III, one can't help but pity mercenary Cooper, who tearfully pleads for the plane to stop for him as the Spinosaurus approaches.
Those poor hunters who were hired by Mr. Ludlow in The Lost World: Jurassic Park. All of them dead, by either T-Rex or raptor jaws and claws, and many of their families now suddenly deprived of their source of income.
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.
Wormtongue finally turns against Saruman and still gets shot by Legolas. This is after a My God, What Have I Done? moment upon seeing the Uruk-hai, and without his involvement in the Scouring of the Shire from the books, which is what actually gets him killed in them.
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.
In X-Men: Apocalypse Angel is the only one of the Four Horsemen killed in battle. Immediately afterwards, Apocalypse dismisses him as weak. This prompts Storm to realise that Apocalypse sees them as little more than minions, and pull a HeelFace Turn.
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, who spends his last few moments hating and hated and trying to take Batman with him, he also comes off as quite pitiable in his malice, and his burial at sea by his own beloved penguins actually comes across as rather moving, no less because they were the only ones who were there for him and his true family. It all has to do with his poignant backstory and very wretched life which is summed up in this funeral so much that he is perhaps one of the evilest examples who is a Tragic Villain and makes this work.
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.
Farmer Vincent who owns Motel Hell spends his last moments lamenting about his hypocrisy in preparing sausages made out of the human flesh of his victims... which in a humorous subversion turns out to be because of using preservatives.
Calvera in The Magnificent Seven goes out trying desperately to understand why. Much of the pathos comes from Eli Wallach being just that good.
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.
"Hey Max... A guy gets on the MTA here in L.A. and dies...think anyone will notice?"
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.
Skyfall: Raoul Silva is a former MI-6 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 couldnt 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.
In Peter Pan, at the very end, Captain Hook has just found himself right over the water, dangling above the crocodile with the last remnants of his fairy dust magic. Desperate to live, he starts thinking of all manner of things that make him happy while the Lost Children and Darlings repeatedly cheer "Old, alone, done for" to bring him down. Then, finally, Hook, sounding horribly depressed and weary, begins to repeat their chant, stops his flailing, and goes straight as he allows himself to fall into the mouth of the crocodile.
The Saeki Family in the Ju-on and The Grudge, or at least Kayako, Toshio, and the cat Mar, who were all murdered by Kayako's husband Takeo under the false assumption Kayako was having an affair. Consumed by their own rage, they now haunt their former home and stalk and kill anyone who enters.
In a way, as everything Sheriff Teasle from First Blood tried to do was to prove what Korean War vets are made of after being shunned for so long and to uphold the law in his duty as a policeman, yet now he's wounded in a pathetic state and is about to take more flak then he's ever before imagined.
The death of ruthless railroad tycoon Mister Morton in Once Upon a Time in the West. An old crippled man who just wanted to see the Pacific Ocean before dying, Morton was willing to have Frank kill anyone who impeded his train's progress. After receiving a mortal wound in his duel with Cheyenne, Morton dies struggling to reach a puddle as a substitute for the Pacific while Frank looks on impassively.
Cato. In the book, he's portrayed as a psycho Blood Knight who enjoys killing other tributes right down to when he dies. Here, he's more or less the same... until he's about to die. We then learn that his motives were to bring honor and respect for him and his District. He was also a career tribute, meaning that he was trained to kill from a very young age, and likely had no choice in the matter. Killing was all he knew. Combining all of these, plus his behavior at the end, implies that he was craving respect and recognition from people, which, in turn, implies that he was abused, neglected, unappreciated, ignored, or possibly all of the above. This may show that he feels the only way to be loved is to win. What's even sadder is, that assumption may have been true.
Cato: Oh no, I can still do this. I can still do this. One... more... kill. It's the only thing I know how to do... to bring pride to my District.
Foxface wasn't really a villain in the book, mostly just being a parasite on the Careers, stealing their food and generally being sneaky. In the movie, we have a scene between her and Katniss where they bump into each other while running from the slaughter at the Cornucopia, look at each other in terror for a second, then silently run off in separate directions. This makes her seem a bit more like Katniss herself. Katniss even seems glum when finding out that Foxface is dead, and from a rather random death too.
As in the original book (and possibly even moreso here), Glimmer in her death scene.
To a certain extent, Seneca Crane. The character seemed to possess a certain degree of honor and fair play judging by his awarding Katniss points and there's something poignant about the scene where he's given a Sadistic Choice wherein his death occurs either way - especially since, like most Capitol citizens, he appeared to be more conditioned into his way of thinking than genuinely evil.
In Part II, we have Michael coldly telling Fredo "You're nothing to me now... You're not a brother. You're not a friend. I don't want to know you or what you do" as Fredo begs and weeps for forgiveness, right before Michael gives the order to kill him(delayed until their Mother's death). While they apparently make amends at their Mother's funeral, he silently affirms his previous order to Al Neri. Further reinforced by the flashback immediately after Fredo gets murdered, in which Tom Hagen and Sonny criticize Michael for opting to join the Marines instead of following in his father's footsteps; Fredo is the only one who supports him.
Michael Dying Alone right after losing his daughter in Part III.
The Professor's death scene in The Bourne Identity. Despite trying to kill Jason Bourne seconds earlier, our hero is horrified to realize he's another Treadstone agent. The audience already knows this, which may fatigue them with exposition. The screenwriter avoids this by injecting humanity into him, so instead of a steely eyed assassin, we meet a very human figure. Bleeding to death slowly, he begins to seemingly babble as Bourne tries to interrogate him, asking Bourne where he comes from, and darkly laughing about their terrible headaches— a result of their mutual behavioral conditioning. In fact, he is not babbling, but seeking commonality in his final moments. Near death, he looks down at his own wound, turns to Bourne and moans his haunting final words, "Look at this. Look at what they make you give." The scene sets a tone for the rest of the movie series. It would initially seem to be about the Professor's lost life, but over the course of the trilogy, with the eventual losses Bourne will endure, the audience sees that he's really talking about his sacrifice of his humanity to his government, and is echoed in the final movie as Jason Bourne's last line.
Jason Bourne: Look at us. Look at what they make you give.
Ravenna's death is played sympathetically, as she is shown to be a Tragic Monster. Once Snow White stabs her, she cowers in a corner to die slowly. Snow stays with her as she does.
In the sequel this goes double for Ravenna's sister Freya. The climax reveals that Freya's villainy was All for Nothing, that she had been duped by her sister and she dies saving the members of her army. Eric and Sara both look sad when she finally passes.
In I Shot Jesse James, the death of outlaw Jesse James is treated as a tragic occurrence and an untimely end for such a legendary bandit. His death hangs over the rest of the film and the guilt of the action haunts his killer Robert Ford, who was Jesse's best friend and saw killing him as the only way to escape the life of an outlaw.
Deep Red: Carlo had to live his whole life depressed and haunted by the memory of his beloved mother stabbing his father to death which meant that the cause of his trauma was also his only emotional support in the world. He covered up her crimes even while she threatened the life of his friend and felt so bound by his feelings for her that he also tried to kill Marc. After his awful end (getting his head crushed by a truck's wheel) a flashback scene to the night of his father's murder shows a horrified little boy who got traumatised for life.
During his monologue at the end of The Incredible Shrinking Man, Scott says that he understands that the spider that he had to kill in self-defence was also just trying to survive.
Ted Bundy: A rather bizarre example, with Ted Bundy's execution being treated as a tragic event despite all his actions up to that point earning him no sympathy whatsoever.
Black Panther (2018): Even after everything he's done, Killmonger's tragic backstory earns him a quiet death, watching the Wakandan sunset with T'Challa. T'Challa even offers to heal him, but Killmonger refuses, asking T'Challa to bury him in the ocean alongside the slaves who jumped from ships in the Transatlantic Slave Trade. T'Challa recognizes that it was Wakanda's neglect that made Killmonger what he was and decides to end the country's isolation policy.
Downfall presents Adolf Hitler as this, astonishingly. While not downplaying or glossing over a single one of his crimes, the film - with the assistance of Bruno Ganz' incredible performance - presents the German dictator as a pitiable figure, like the captain of a doomed ship, putting on a brave face as the Red Army tightens the noose on Berlin and the folly and cruelty of his philosophy (along with the ethnostate he built on the bones of millions) crashes down around him. The film was controversial among critics and reviewers, several of whom questioned whether it was morally acceptable to present him in this manner.
Roger Ebert: "Admiration I did not feel. Sympathy I felt in the sense that I would feel it for a rabid dog, while accepting that it must be destroyed."