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.
In 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.
Kadaj from Final Fantasy VII: Advent Children, whose main motivation was to be with his "mother". He's at least welcomed into the afterlife by Aerith's spirit.
While Cobra Commander was always an ineffectual coward in G.I. Joe: A Real American Hero, one can't help but feel for him in G.I. Joe: The Movie where he is lying on the ground, in agonizing pain, having been exposed to virulent spores that are mutating him into a snake, and slowly losing his mind.
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 LEGO Movie 2: The Second Part: Upon realizing that his friends coming back to save him means that he will have never existed in the first place, Rex calmly accepts his fate and gives Emmet some reassuring final words before vanishing into nonexistence with a smile on his face.
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.
Even Zira counts as she fell to her watery grave after refusing to let Kiara rescue her, something which Kiara didn't expect; even Kovu is very discomforted by this as he sighs very sadly watching his hated mother drown to her death despite everything that she has done.
In The Prince of Egypt, one of the most tragic examples is presented with Rameses. After Moses has successfully led his people across the Red Sea and to safety from Rameses and the Egyptians, Moses hears Rameses across the sea screaming for his brother in anguish, rage, and sadness. Rameses pride and his obsession with living up to his father's legacy led to the destruction of his kingdom, the loss of his son, and now the loss of his brother. Moses feels nothing but sadness and pity towards his brother in the end.
The Baker's Dozen in Puss in Boots: The Last Wish serve Big Jack Horner for his pie business, and their demises are played for Black Comedy. Despite this, however, Jack's treatment of them is taken seriously. This is first shown when Jack tries to shoot unicorn horns at Puss, only to be end up striking some of his bakers by accident and causing them to explode in confetti; even Puss himself is completely shocked by this. The Ethical Bug is also shocked to see a majority of the bakers falling to their gruesome deaths on a cliff, which prompts him to declare Jack "an irredeemable monster" for this. Even the last remaining member ends up being disintegrated by the Wishing Star's barrier, all because of Horner's refusal to pay attention to her.
Hun in Turtles Forever, after the Turtles finally convince him that the Shredder is going to destroyThe 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.
Up: Even if Charles Muntz was an Ax-Crazy narcissist, all he wanted was to restore his reputation by proving he was right about the bird all along, and Carl still saw him as an inspiration in his life even when he became a laughingstock. Thus, when Muntz falls to his death, Carl takes absolutely no pleasure from it.
Wonder Woman (2009): Persephone may have killed innocent people and nearly brought about an international war, but her death at the hands of Hippolyta is played very sadly. Her Shut Up, Kirk! to the queen is said in a very tragic tone.
"The Amazons are warriors. But we are women too."
Wreck-It Ralph: King Candy/Turbo's death. While he is an evil and selfish asshole who 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.
Live-Action
HAL 9000 in 2001: A Space Odyssey. Despite being an apparently cold, logical computer AI who is 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 lobotomized 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..."
In Alien: Resurrection, for all the murderous havoc the Newborn and its entire race caused for Ripley, she's visibly sorrowful about having to kill it (and in an indirectly torturous manner at that).
The Babysitter (2017): Even though she's a crazy cultist who made a Deal with the Devil, Bee's death is still genuinely sad. In spite of everything she did, she really did care about Cole, and even saved his life. She explains that she made the deal and began sacrificing people because before, she used to be small and scared... like Cole. When he rejects her offer to join her and share her power, instead burning the Devil's book and running her over with a car, they still have one last heartfelt conversation, where Cole admits that he always viewed the two of them as a team. Bee sadly acknowledges that she's the bad guy, and tries to recreate their usual goodbye ("See ya, C." "See ya, Bee.") one last time. Cole simply says "Goodbye" and walks away, leaving her to cry just before she passes away.
The Penguin in Batman Returns. Even though he's a hideous 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.
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.
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 Bourne Ultimatum as Jason Bourne's last line.
Jason Bourne: Look at us. Look at what they make you give.
Whilst not villainous per se, Dr. Hoernbeck in the Animal PlanetMockumentaryThe Cannibal in the Jungle off-handedly speculates that the Ebu Goro (surviving Homo floresiensis) may be dying out due to habitat loss, making their fate semi-tragic.
The Tyrannosaurus rex in Carnosaur is a human-killing carnivorous dinosaur which was created by Doctor Jane Tiptree and unleashed upon the local countryside alongside other dinosaurs, going on a killing spree. The T.rex is eventually Gutted Like a Fish by Doc's Bobcat, and although it's not seen as sympathetic by any character in the film besides Tiptree (in a twisted way), its final moments are played over somber music while it makes some really sad-sounding whines as it slowly dies from its injuries.
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.
Vincent from Collateral gives a rather saddening Meaningful Echo just before he dies at the end of the film.
"Hey, Max... A guy gets on the MTA here in L.A. and dies... think anyone will notice?"
In The Dark Knight, Harvey Dent. Lost his love, half his face, got his mind completely screwed by The Joker, who destroys what remains of his sanity and drives him into anti-nihilistic despair, and almost end up destroying his life's work, and killing an innocent child. Even he feels he is too far gone (he puts the gun on himself before the kid, clearly hoping the coin will doom him), but is unable to stop, so Batman has to stop him, and ends up dying for it. Luckily, Batman and Gordon manage to save his good work and clean Gotham.
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.
Starro the Conqueror in The Suicide Squad. Sure, he goes on a rampage and ends up turning thousands of people into possessed zombies, but that's only because he was lashing out in anger due to thirty years of imprisonment and torture brought upon by the Thinker and the United States Government. After Harley Quinn pierces his eye and leaves Ratcatcher's rats to eat his internal organs, Starro spends his last moments remembering his life before being captured, where he was just an aimless wanderer looking at the endless beauty of space.
"I was happy... floating... gazing at the stars..."
Death Line: The 'Man' is highly dangerous, but also deeply pathetic given his deformities, inarticulacy, and his obvious grief when the 'Woman' dies.
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 traumatized for life.
Downfall (2004) 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.
The death of Riley Biers in Eclipse. In his final moments, he calls out for his lover, Victoria, only for her to ignore him.
In The Faculty, Casey kills the alien queen, Marybeth. As she is dying, he softly tells her, "You wouldn't have liked it here anyway.", acknowledging that — despite being a monstrous parasitic alien — she was just another outcast trying to find her place.
In 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 than he's ever before imagined.
The Fly (1986): Since the entire movie follows Seth Brundle's Protagonist Journey to Villain "Brundlefly", this trope is inevitable. His selfish, sometimes brutal actions in the second act (after his Teleporter Accident but before the Internal Reveal) are in hindsight part of a Split-Personality Takeover, not just his feeling Drunk with Power; he subsequently realizes and explains that he's inevitably going to become a villain because the insect side of him has "no compassion, no compromise." The process is just sped up by his learning that his lover Veronica hasn't told him she's pregnant with his probably-mutant child and wants to abort it, and sought the help of her ex-lover Stathis to do so... said ex-lover being indirectly responsible for Seth's Tragic Mistake in the first place. (Seth believed she was cheating on him with Stathis, got drunk, and impulsively decided to become Professor Guinea Pig.) In the climax, he maims Stathis and attempts Romantic Fusion with Veronica and their unborn child, with his One-Winged Angel transformation symbolically happening as he drags her to a telepod. Luckily for everyone else Laser-Guided Karma kicks in and renders him a pathetic, helplessly Clipped-Wing Angel whom a sobbing Veronica has to Mercy Kill at his silent request. The filmmakers were so intent on pulling off this trope that they cut first a storyboarded scene in which he killed and ate a bag lady (though he showed remorse afterward), and come the test screening stage an entire reel that had him creating a fusion of a cat and baboon that he subsequently slew because audiences stopped caring about him after that. The final result? The intended "Ray of Hope" Ending (actually, four different versions of one) that would have given closure to Veronica's story had to be cut because audiences were too upset by Seth's death to care.
Ghost (1990): Willie Lopez and Carl Bruner. The scenes of them being literally dragged into the netherworld (and what is probably waiting for them once they get there) are pitiful and terrifying.
Carl: Sam? Sam: Oh, Carl...
Most of the Corleone family go out this way in The Godfather:
Sonny Corleone in Part I, particularly with Vito's and Tom Hagen's reactions.
Vito:[crying] Look at the way they massacred my boy...
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.
It goes all the way back to the original Godzilla (1954); 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 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 Godzilla (1998) 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.
In Godzilla (2014), 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.
Godzilla vs. Kong: Not in the film, but in the novelization, Ren Serizawa has this as his consciousness is being devoured by Mechagodzilla's new consciousness. One of the last things he sees is his father's face (his father's death was the reason he turned evil, according to the novel), and Ren thinks "Dad? Daddy?" before the memory is disintegrated.
Harry Potter and the Deathly Hallows: Part 2: Voldemort's death scene accents this pretty well. His life ends with him in visible despair at the realization that his last Horcrux has been destroyed and he's surely going to die (the very fate he committed his entire life to permanently staving off no matter the cost to his very soul). A triumphant yet bittersweet score plays over the scene, emphasizing his melancholic but deserved fate.
Hobo with a Shotgun: Slick gets a surprisingly emotional send-off when he calls his father begging for help, and they end up comforting each other before he dies. However, this is a downplayed example, considering that we just saw him torch a whole bus full of children.
Home Sweet Home (2005): The film's "monster", who abducted May's only son and brainwashed the kid into turning on his own mother, turns out to be a mentally ill woman who lost her family years ago and stole the child for herself in order to replace her deceased child. Her eventual Redemption Equals Death moment when she takes the plunge off a balcony is absolutely played for drama.
Hook gets this in his last moments, before the Lost Children wind up chasing him into the square where the Croc falls on him. Hook kind of spoils it, though.
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 more so 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 in which he's given a Sadistic Choice wherein his death occurs either way — especially since, like most Capitol citizens, he appears to be more conditioned into his way of thinking than genuinely evil.
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-defense was also just trying to survive.
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."
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.
Die Another Day: Bond experiences this when he sees Miranda Frost's corpse even though he had tried to kill her the instant he had learned that she was the traitor at MI6.
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" Remark 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.
The Saeki Family in 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.
More of an "Alas, Poor Mooks", but 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. Worse still is that the movie tries to set up the whole team as a bunch of sinister, dog-kicking baddies, but Dieter is the only one to really fit that mold; the rest are either depicted sympathetically (like Roland and Ajay) or as just regular guys doing a job.
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.
Kill Bill: Bill is killed by the Bride after a very short fight, using the Five Point Palm Exploding Heart Technique taught to her by Pai Mei. Bill tenderly tells her that she is still the love of his life even after everything that happened between them, then casually stands up, adjusts his coat, takes six steps and collapses dead. Even the Bride cries at his death.
Kill the Irishman: Real-life Irish mobster Danny Greene tries to make peace with the Mafia and get out of the gangster business to retire in Texas. But the Mafia wants his head. The orphan who had a tough life is eventually killed with a car bomb, still Defiant to the End when he sees his killer point a gun finger at him.
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."
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."
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.
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.
The Magnificent Seven (1960): Calvera is the leader of a group of bandits who annually rob a villa. He has spared the gunmen hired by the village (and betrayed by their employers) only to see them return and save the town. Calvera dies desperately trying to understand why. Much of the pathos comes from Eli Wallach being just that good.
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.
Avengers: Endgame presents a Thanos who hasn't regretted killing half the universe and even destroyed the Infinity Stones so his actions won't be undone, but his death is still a slightly sad scene, especially given it happens after he tells Nebula that he's beginning to think he treated her too harshly. The time-travelling Thanos intent on destroying everything also gets to experience the despair of the victims once his army ends up on the receiving end of the snap: after seeing his forces crumble into dust, including one of his lieutenants reaching in confusion and terror, Thanos seeing his disintegration is next, looks up with an expression of pure agony as he slowly lowers his head; eyes closing, and body sulking down to the ground silently.
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.
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.
Nicholas and Alexandra: Nicholas II was definitely a terrible leader who hurt his people... but being brutally and violently executed along with his wife and innocent children is not a good way to go.
The death of ruthless railroad tycoon Mister Morton in Once Upon a Time in the West. An old crippled man who just wants to see the Pacific Ocean before dying, Morton is willing to have Frank kill anyone who impedes 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.
Oldboy (2003): Right before Woo-jin commits suicide, we have a sad flashback to when his sister jumped into the dam. Quentin Tarantino was at a screening of the film, and was shocked to find himself crying for a character who had been completely despicable for the entire prior duration of the movie.
In The Outlaw Josey Wales, there is the unnamed Bounty Hunter who comes after Wales and finally meets his end at the hands of his mark in Santo Rio. The guy steps into the saloon and confronts Wales, walks out and then walks back in again after a moment (realizing he couldn't live with the cowardice) even though he sounds like he knows Wales will kill him ("I had to come back."). Wales blows the man away and seems to think of it as a Senseless Waste of Human Life.
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 (mostly just blood and gore and death) 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.
Pirates of the Caribbean: The Curse of the Black Pearl: Barbossa falls with the final line "I feel... cold...", and mournful violins play as his crew realize they're no longer cursed but ironically also no longer immortal, and they're immediately taken into Navy custody to be executed by hanging.
Pirates of the Caribbean: At World's End gives us one for the Kraken, whose massive corpse stranded on a beach gets Captains Sparrow (who was killed by it in the last movie) 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.
Dawn of the Planet of the Apes has a downplayed, but still notable example with Koba. Driven to becoming a cruel and ruthless tyrant and murderer of humans and apes alike by his tortured history as a lab ape, Koba is dropped to his death by Caesar for his crimes against both species. While Koba definitely deserved (and needed) to die for the lines he crossed, his death still has a sad aspect to it. Koba was once a good and loyal friend to Caesar before his fear and hatred of humans led him to usurp Caesar due to the latter's decision to work with them to ensure peace between humans and apes. Because of their past friendship, Caesar is clearly not happy to execute Koba, and no one takes joy or satisfaction from Koba's demise (in fact the novelization outright describes the apes as mourning Koba despite his crimes).
Sadako Yamamura 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 bonds 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 adaptation, 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. Then she gets trapped in the well again at the hands of Naomi Watts.
Gen. Francis X. Hummel from The Rock. The fact that he's actually an Anti-Villain makes you feel even more sorry for him when he dies.
Tony Montana in Scarface (1983). After becoming drunk on power, Tony has lost much of his humanity, but his ending is pretty sad to see, especially since he's willing to sabotage an assassination mission in order to save the lives of two innocent children, which eventually leads to his own downfall and death.
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.
Robert Webber manages to turn his last scene in The Silencers into one of these.
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.
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.
Prince Astaroth of Sodom and Gomorrah may be utterly corrupt and ruthless in his hunger for power and women, willing to ally himself with an enemy tribe to achieve the former and refusing to take "no" for an answer in pursuit of the latter, but he becomes a sympathetic figure in his final moments. When Lot disarms him during their Duel to the Death, he pleads for mercy in Jehovah's name, but Lot cannot think through the rage of having his Relative Button pressed and kills him anyway. Lot's distraught daughters, Shuah and Maleb, rush to his side, and he manages a smile as he expresses gratitude for at least being able to die in their arms.
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.
Shinzon from Star Trek: Nemesis. While not considered 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 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.
Darth Vader's death is probably one of the most famous examples of this trope. It does not fall until Return of the Jedi, when one actually realizes how bad Vader's life is, and the fact deep down he regrets who he became. He does manage to redeem himself, and dies in the arms of his son as Anakin Skywalker.
Jango Fett in Attack of the Clones. Sure, he's a cold-blooded killer who tried to assassinate a Republic senator and kill a Jedi, but he did so just to make ends meet for his family. It's even more heartbreaking when you consider Jango's mistakes results in poor Boba having to fend for himself.
Count Dooku in Revenge of the Sith. He was a monster, but the way he dies, being betrayed by his master (to whom he was loyal), and left defenseless, makes one feel at least some sadness for him.
Nute Gunray and the Separatist council. They were some of the most unlikable characters of the saga, but the way they are betrayed and killed (and, unlike with Dooku, they were doomed when Vader entered the room) does not make one joyful, considering the bigger evil is also the one killing them.
All the main villains in the prequel trilogy (except Palpatine/Sidious and General Grievousnote He did have a sympathetic backstory in the Legends continuity, but most of that now falls under Canon Discontinuity after the Continuity Reboot. Canon Grievous has no redeeming qualities, nor is his death portrayed in a sympathetic way.) end up being pitiful in a way, considering they were all tools for the dark lord, and became discarded once useless. And the only one who was not discarded (Anakin) ended up even way worse than dead (Lost everyone who loved, burned and mutilated, trapped in a mechanical suit isolated from the rest of the world, as an enforcer of evil, and knowing all his crimes were for naught).
Solo: Beckett meets his death at the end of Han's blaster, but it's not portrayed as much of a victory.
Ironically subverted in 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.
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.
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 realize that Apocalypse sees them as little more than minions and pull a Heel–Face Turn.
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.