Seeing clearer what I've done I'd refuse to let things go I could never once admit I'm wrong And what do I have to show? Seeing clearer what's at stake And the things I have to change I just hope I can, it's not too late To get a chance to end this pain
It's impossible to tell how many of these Akito from Fruits Basket has. When Hatsuharu almost beats her up for imprisoning Rin, during conversations about Shigure and Ren's relationship, when she stabs Kureno, and when Tohru falls from a cliff in front of her. She consequently goes through a very angsty, somewhat suicidal, phase. She ends up being saved from herself by Tohru's friendship and Momiji's statement that Akito should treasure the ones she cares for.
In Angel Beats!, Otonashi defeats Naoi by forcing him to face that in the end he was ultimately responsible for his own misery; Naoi's motivation stemmed partly from his belief that his life had been empty, and Otonashi forced him to realize that Naoi could only blame himself for that.
Magical Project S: Pixy Misa, the evil magical girl, was overpowering and about to kill the heroine but entered a BSOD when she realised she was about to hurt her loved ones too and reverted to her powerless alter ego.
Banestone/Sesshouseki possessors in Ga-Rei Zero- are prone to this, Mei's powers fail occasionally, while Yomi reverts to her non-evil side long enough to realize what she's doing. Both have My God, What Have I Done? moments during their BSODs (Yomi tries to take responsibility and attempt suicide, while Mei just panics) until their Sesshouseki kick in again.
Digimon Adventure 02's Digimon Emperor/Kaiser when he realizes that Digimon are real, and Wormmon has just made a Heroic Sacrifice to stop him, the boy freaks out, throwing away his costume, crying, and screaming that he's sorry before wandering alone into the desert.
In Digimon Tamers, this happens to Beelzemon, the Mega form of the human-hating Digimon, Impmon. After being granted the power to digivolve like he always wanted, Beelzemon attacked the children and destroyed one of their partners (who unfortunately, don't have the pleasure of being reborn as digi-eggs as it was in the previous series). After being defeated in battle and spared, he begins to come to realize the atrocities he had committed and wanders around, guilt-ridden, depressed and haunted by memories of what he did. After surviving what was essentially a suicide attempt (not fighting back when he's attacked by a swarm of digimon which quickly render him powerless), he eventually sets off to make things right, by first making amends with the humans he had abandoned and then by helping the others in the battle against the D-Reaper, and saving the girl who's partner he killed.
Self-inflicted (of sorts) example with Greed in Fullmetal Alchemist. The second version of him, while having mostly the same personality, is at first much more malicious in keeping with the behavior of the other homunculi who are The Heartless. After Greed kills Bido, who was the only surviving member of his former True Companions after the rest were slaughtered by Bradley, Greed's memories return and Ling starts mocking Greed in his head while he's tormented by the memory of his comrade's screaming voices. While this also counts for Amnesiac Dissonance, it fits this too, because the Power of Friendship is used as a weapon against him.
Envy experiences this when Ed points out the entire reason he was so vicious and hateful of humanity was his jealousy of their ability to rely upon one another, while Envy was all alone. He begins weeping in frustration at having a human, and the one he despised most of all at that, understand him so deeply and commits suicide rather than deal with the humiliation.
Havoc got a more permanent one — after losing her powers when Heaven's Gate collapsed, she got all her emotions back. Which is a bit of a problem when your power is to create wide-scale Explosive Decompression, and your renumeration is to drink the blood of children. The only way she got anywhere near Hell's Gate was after making Hei promise to kill her should her powers — and her old mindset — return.
Cyrus in Pokémon: Diamond and Pearl Adventure has a BSOD for most of a chapter when he realizes that his grand plan to fix the world (by destroying and rebuilding it, natch) only managed to summon a pair of very angry gods whose fight will destroy everything without any hope of revival. Even near the end when he manages to get his act together, the impact of all this leaves him drained to the point where one of his officers has to help him stand.
Colress gets one in the anime after his mind control machine breaks. He gets better.
Tsubame Otorii of Cyber Team in Akihabara. Since her introduction, she acts as the Dragon to the Big Bad, easily defeating the Cyber Team girls in every encounter. In episode 20, Tsubame is dragged home by Hibari. She spends the entire episode slowly breaking down while watching how Hibari's family interacts with one another, eventually suffering a Villainous BSOD and freakout by the credits, followed by a Heel-Face Turn in the next episode. The episode is also one long Tear Jerker, as we see how horrible a childhood Tsubame actually has had up to this point.
In TOKYO TRIBE 2, Buppa has one of these in episode 10 when Mera stabs him in the face. He stays in that state for nearly an episode before seeing Sunmi snaps him out of his BSOD. When someone points this out, he simply denies that the BSOD even happened.
Anemone of Eureka Seven begins this after her second failure against the Nirvash, due to her fear that Dewey will kill her for failing. This causes her to do nothing but lie down in her bed when she isn't fighting, and she gets worse after finding out Dominic went AWOL.
In the 11th Haruhi Suzumiya novel, Kyouko Tachibana has one when she realizes how bad the goal she's been working toward really is, and when her two teammates decide that they want to KILL Haruhi to accomplish it. This naturally leads to her Heel-Face Turn.
In Gankutsuou, Fernand Morcef's response to losing virtually everything he has worked and sacrificed for including and especially his conscience and morality due to Edmond Dante's successful revenge is taking down his planet with him as he crashes and burns. Even if it means rejecting a Last-Second Chance offered by his wife, despite the fact that it was his Love Makes You Evil for her which ultimately caused his Start of Darkness.
Anti-Villain Coyote Stark from Bleach has two of these. A powerful but lonely arrancar who considered the other Espada his True Companions, Stark can't bring himself to try in his fights after his immediate peer Barragan is killed, but his companion (and other half) Lilynette snaps him out of it, convincing him to avenge Barragan instead. In the anime, however, Lilynette's consciousness is destroyed by Taking the Bullet for Stark, which clearly destroys his will to fight, and to live; moments later, Stark's opponent and Good Counterpart Kyoraku cuts him down as well.
In Mobile Suit Gundam, Degwin Zabi suffers this after his youngest son, Garma, is killed. By the end, he's had enough of the war and wants it to end. In the anime, he attempts to broker peace only for Ghiren to blast him and General Revil with the Solar Ray. The novel of the series, however, doesn't give him that chance - he can only watch as the rest of his children get plucked off before Char takes over.
In Star Blazers, Comet Empire series, in one of the episodes close to the end. Leader Desslock had earlier accepted a commission from Prince Zordar to defeat the Star Force, so he pins the Yamato by teleporting mines over to surround it. To escape, the Yamato executes a small warp and rams Desslock's ship. Deputy Captain Derek Wildstar boards the Leader's ship. The two of them face off on the bridge. Desslock slowly levels his pistol at Wildstar, while goading Wildstar to shoot him. But Wildstar, already injured earlier, falls to the deck while drawing his. His love interest, Nova, dashes out of hiding, grabs the pistol, blocks Desslock's aim, then aims Derek's pistol at Desslock. Moments later, she drops the pistol, places Derek's head in her lap, and comforts him while he remains semiconscious. Desslock gets his Villainous BSOD as he witnesses Nova's simultaneous display of extreme bravery and extreme devotion. It makes him change his mind about pursuing the Star Force, he declares to Nova that the war between Gamillon and Earth is over, and he offers her advice on the Comet Empire's one weak point in its mobile fortress. Doubles as a Crowning Moment Of Awesome AND a Crowning Moment of Heartwarming!
Seto Kaiba of Yu-Gi-Oh! had one of these as well, over the course of the first half of the second series' first season. Back then, prior to the end of the first episode, Kaiba didn't take dueling seriously at all and believed that power was the only way to win a game. Then he received a big shock when Yami summoned Exodia the Forbidden One and obliterated all three of his Blue-Eyes White Dragons (which at the same time led to Mokuba using a "This Cannot Be!" line) and afterwards used Mind Crush on him. Ever since then, Kaiba came to realization that he didn't know who he himself was anymore, and began to seek redemption. He eventually learned that Mokuba was taken prisoner by Pegasus and went to rescue him only for both's souls to be captured by Pegasus later... until Yami finally won his duel with him with the help of his friends.
Annie Leonhart breaks down more than once, when forced to confront the innocent lives lost due to their actions. The first time, at Trost, she begins apologizing with a vacant expression to the body of her friend, Mina. The second time, she is horrified when she sees her fight with Eren has crushed civilians.
Overcome with stress, Reiner Braun breaks down and confesses to their crimes. Breaking down in tears, they claim to have just been stupid kids that didn't understand anything and worries their friends have made them weak. But even though their moral compass has been lost, they conclude they've come too far and have no choice but to see things through. He's later revealed to have experienced such guilt over his actions that he suffers from episodes of Trauma-Induced Amnesia.
Bertolt Hoover finally breaks down when confronted by the others, who invoke The Power of Friendship in an effort to defuse the situation. He begins to cry Tears of Remorse and admits to having been happy during his time with them, but knows his actions cannot be forgiven. Still, he refuses their Last-Second Chance and tells them he doesn't have a choice.
During his climatic fight with Joseph, Wamuu is tricked into a set-up that shreds his arms to the point they're only attached by a couple of sinews. He nearly goes catatonic for a while as he realizes just how badly he was Out-Gambitted, only snapping out of it by putting out his own eyes (forcing him to rely on other senses that can't be tricked as easily).
One arc of The Authority has the heroes forced to give the previous The Doctor (a mass murderer) his powers back for an hour, during which he one handedly thrashes the team. The current Doctor is berated because the old Doctor can alter time to make his one hour infinite, but as it turns out each Doctor is the sum of all previous ones, and that made the old one gain the new one's conscience. He realizes the horror he's done, begs for forgiveness, and is then killed point blank (The Authority are like that).
In Devil's Due's G.I. Joe vs. the Transformers, Serpent O.R. captures Optimus Prime to gain access to the Matrix of Leadership. When he achieves this, he becomes enlightened to just how horrible the things he's doing are, and tries to have himself destroyed. Then Cobra Commander hijacks his body from Earth, and to stop him, Hawk has to expose both himself and the Commander to the Matrix. The revelation breaks Cobra Commander's mind.
There was one DCU story where all the people on earth were depowered. The Joker became sane as a result, and committed suicide over the guilt of everything he'd done.
Joker also gets one towards the end of The Killing Joke. He genuinely doesn't understand why he couldn't break Gordon or why Batman is still coming at him. He stops smiling and pitifully asks "Why aren't you laughing?" right before Bruce smashes through a wall and brings him back to the here and now.
The DC ComicsElseworlds story Superman: Red Son ends with Superman and Brainiac leading a Soviet invasion of Washington DC. President Lex Luthor stops Superman by sending him a written message: "Why don't you just put the whole WORLD in a BOTTLE, Superman?", a not-so-subtle reference to the city of Kandor Stalingrad. Superman immediately breaks down.
Lex himself gets one near the climax of All-Star Superman. After a day of having Superman's powers, and knowing they're already fading, it finally sinks in to Lex that all he's done with them is blow stuff up.
In ElfQuest, this is Winnowill's reaction when Leetah tries to heal her, forcing her to relive her memories of how and why she turned to evil, and of everything she's done since. Too proud to spend the rest of eternity angsting and atoning for it all, Winnowill tries to kill herself.
The Ghost Rider's Penance Stare makes a person feel all the suffering that they had inflicted upon innocents. This oftentimes leaves them catatonic.
And he once even got to use it on Galactus.
Magneto had a well-done example of one mixed with a What Have I Done moment when he believed that he had accidentally killed Kitty Pryde (Kitty actually had just been knocked unconscious due to massive feedback between her phasing and Magneto's powers). It could well mark the beginning of a Heel-Face Turn that culminated with him some 50 issues later taking over the X-Men from Professor X.
In Star Wars: Tales of the Jedi, Ulic Qel Droma suffers a rather massive one when he murders his own brother in a fit of rage. Before he had only been redeemed by the delusion that he was doing the right thing. After killing Cay, Ulic finally faces what he's become and simply breaks down sobbing while cradling his brother's corpse. Ironically, crossing the Moral Event Horizon finally forced him to change for the better. Raana Tey also undergoes this. After suffering an increasing breakdown over 12 issues, committing a multitude of atrocities against the protagonist, her plans go to hell, and when she's trapped Zayne tries to save her despite all the things she's done. This causes Raana to realize that she's the villain and not Zayne, and that he is in fact not the monster she think's he is. She dies less then a minute later, and her last words are essentially a plea for forgiveness from her mistress and from Zayne.
The conclusion of KnightsEnd has Batman force Jean-Paul Valley to dump his armored Batsuit to confront him then blind him with Night Vision-enhanced sunlight, forcing Jean-Paul to finally remove the mask. Weary and defeated, Jean-Paul can only say one thing:
Jean-Paul: "You're Batman. You've always been Batman. And I am nothing."
In the Iron Man arc The Secret Origin of Tony Stark, the rogue Rigellian Recorder robot (try saying that five times fast) designated 451 reveals he has been laboring for 500 years to place humanity - Earthlings - in a position where they can create a galaxy- or even universe-wide empire of harmony and peace. To this end he wishes them to give the ultimate deterrent to keep everyone who would destroy them at bay - Godkiller, arguably the ultimate weapon of mass destruction. The final piece was a pilot - to which end he had genetically engineered one human to be such. When Tony Stark - of course - is forced to interface with Godkiller, he and 451 discover that the system does not recognize him because he's adopted. The interface does not work. When 451 realizes he has worked for five centuries and has directly or indirectly killed over 450,000,000 people for nothing he slumps down and stammers "One should not have acted".
In Flashpoint, the Joker aka Martha Wayne is so horrified when she finds out that in the timeline where Bruce survived instead of her and Thomas, he becomes Batman (with all the misery that entails) that she loses any remaining sanity and is Driven to Suicide.
In Trinity War, Vandal Savage tries to open Pandora's Box, a box that can only be opened by someone who is either purely good or purely evil. It turns out that even Vandal, who practically invented evil as a human concept, isn't evil enough to open the box. Instead, the box's power unleashes all of Vandal's deeply repressed guilt over his sins and leaves him a weeping broken man.
In the Kim Possible fanfic Spirit of Snow, Monkey Fist goes through this in the present day scenes after his actions lead to the "deaths" of his lover and unborn child, and Sensei helps him get through it. An interesting example in that he is in a BSOD from the very first chapter, and that the story is told through a series of flashbacks interwoven with the present day scenes to show how he got to this point.
In the Death Note fic A Cure for Love Light after he loses L in both the deleted scenes and in the main story. It's the variation where "the villain becomes more dangerous" as Light goes off the Morality Chain.
Another Friendship Is Magic example happens in Why?, which elaborates on Discord's one from canon and makes it an even bigger example; when Discord realized how much it hurt to almost lose a friend, he realized what it must have felt like for the Mane Six when he broke their friendship apart.
Gru, the Anti-Villain Protagonist of Despicable Me goes into a deep depression after his Dragon Dr. Nefario sends the girls he's adopted and just recently bonded with back to the orphanage so that he could focus on their plans to steal the moon.
Scar in The Lion King undergoes a very brief one when Simba returns, mistaking him for Mufasa (his tone implying guilt or at the very least fear):
Scar: Mufasa? No, you're dead...
In The LEGO Movie, President/Lord Business undergoes one when Emmet tells him that he is not the bad guy.
Films — Live-Action
The film adaptation of Harry Potter and the Deathly Hallows does have Voldemort briefly experiencing the trope whenever his horcruxes are being destroyed (in one instance, when he was bombarding Hogwart's barrier with spells, after firing a huge beam from his wand upon a horcrux being destroyed, he stares in shock, looks at his arm, and leaves without a word. Both the movie and the novel also imply that this is the reason why Harry and his friends were able to track down the remaining horcruxes.
The Ghost Rider movie fits this trope, since the Big Bad was soulless (and thus immune to GR's Penance Stare) until the movie's climax.
The Operative from Serenity, when shown what the Alliance did at Miranda.
Mal: They take you down, I don't expect to grieve overmuch. Likely to kill you myself, I see you again.
The Operative: You won't. There is nothing left to see.
Watchmen (specifically the film): Ozymandias appears to be going through one of these the last time he's seen on camera. He lets Nite Owl beat him, without even the slightest move to fight back this time, and then wanders over to watch the others leave while staring into space, stoop-shouldered and weak-looking. It's a bit complicated, given that his mass murder actually saved the world from a greater threat, but unlike in the comic, he can't just calmly meditate on his utopia, and in the sped-up footage showing New York being rebuilt, it's possible to pick out Veidt Enterprises building equipment taking care of things.
The 3rd Saw movie was supposed to have this. Jigsaw was to awaken on his makeshift hospital bed, and realize to his horror that for all his life before the films, for all his warped intent to try to make people reflect on what they've done with their lives, all that anyone would remember him as is a monster and a killer. The thought, naturally, was to have occurred too late in the film for him to do anything to save the current protagonist, leaving the man weeping and too weak to move. What Could Have Been, indeed? A slasher movie villain feeling remorse for his crimes could arguably have redeemed the series from shallow Gorn.
Cutler Beckett suffers this in his final moments in Pirates of the Caribbean: At Worlds End, when both the Black Pearl and the Flying Dutchman actually flank both sides of his ship: When he witnesses this, he couldn't even give the order to fire, as he was rendered virtually catatonic from witnessing it, and could only reply in a very soft but shocked tone "It's just... good business...", and walked, not ran, but walked as his crew abandoned ship and his ship was being destroyed, and couldn't even react when the flames from the ship exploding engulfed him.
This is despite the fact that his ship has more guns than the Pearl and the Dutchman put together. On the other hand, the Dutchman can't be sunk. And really, if a pair of ghost ships suddenly stopped fighting each other and decided to team up against you, soul-crushing fear is an understandable reaction.
Davey Jones tried to avoid this by removing his heart.
Barbossa's in the first movie is nicely understated. The apple may be a bit much, though.
Blackbeard when Jack reveals that he gave the the chalice with the mermaid's tear to Angelica instead of him.
Darth Vader in the Star Wars saga could be said to be in one for the entire Original Trilogy. The unenergetic, almost catatonic way he goes about his duties is quite a contrast to the fiery passion he had before Padme's death. It takes seeing his son brutally tortured by the Emperor to finally snap him back to his senses.
In Skyfall, Silva is at last about to fulfill his Roaring Rampage of Revenge, as he holds the mortally wounded M in his grasp and puts his gun to her face...before he starts crying and puts the gun in M's own hand, presses his temple against hers, then guides the gun to her other temple, and he begs her to kill them both with the same bullet.
Caine from the Gone series, during the period between Gone and Hunger.
Galbatorix in the final novel of Inheritance Cycle ...and how! Eragon channels his Applied Phlebotinum to force Galby to understand the suffering his actions has caused - a whole century's worth of it. Galbatorix promptly turns himself into a literal nuclear bomb, complete with earth-shattering explosion and massive radiation fallout.
In Harry Potter and the Deathly Hallows, it is mentioned that a Horcrux can be destroyed and a Soul made whole if its creator feels enough regret, which may be fatal to him. In a twist, it is done the old-fashioned way after all.
On the other hand, in The Tales of Beedle the Bard, one story ("The Warlock's Hairy Heart") does end this way. It has commentary from Albus Dumbledore explaining it.
Since Death tends to show up after people have been disconnected from all their glands and after death has stripped away any rose-tinted glasses villains may have had about their actions, he's been known to induce a few. Mr. Tulip gets a big one in The Truth (although he's probably better off than his associate Mr. Pin who didn't repent).
When Inspector Javert from Les Misérables finds that Jean Valjean, while still a criminal, is a good person, Javert simply cannot reconcile his previous black and white system of morality with this demonstration that all along he had been wrong in his belief that what is lawful and what is right were one and the same. He jumps off a bridge and drowns. His final song in the musical is essentially a summation of his Villainous BSOD.
Very common in Warhammer 40,000 among people tainted by Chaos, when Chaos ceases to blind them:
In Sandy Mitchell's Ciaphas Cain novel Cain's Last Stand, the Sisters of Battle completely lose control after Jurgen's blank status frees them from mind-control; they jump to their deaths.
In Graham McNeill's Horus Heresy novel False Gods, when Horus mortally wounds Temba, Temba recovers from the Chaos taint, realizes the scale of his betrayal, and sobs.
A hideously dark version in Age of Darkness. A failed Care Bear Stare attempts to turn Kharn of the World Eaters back to the loyalist side. It fails when Kharn realises this, but the important thing is that the loyalist Thousand Son who tried knows that Kharn will now always live with the knowledge that siding with Horus (and Chaos) was wrong and that he could have willingly turned back. The loyal Thousand Son briefly wonders what effect this will have on Kharn in the future before dying. 10,000 years later and Kharn is well known for being psychopathically angry (even for a World Eater) and, most interestingly, perfectly willing to slaughter his own comrades...
Much of Death Star's cast go through a Heel Realization by the time Alderaan is destroyed, and most of them go on to defect. Tenn Graneet, the head gunner on the Death Star, didn't, but he found that pulling the trigger brought him misery beyond his ugliest dreams. At the Battle of Yavin, the superlaser actually was ready to fire, but he stalled desperately until Luke's proton torpedoes hit home.
He wouldn't be able to walk on a street on any civilized planet on the galaxy; people wouldn't be able to abide his presence. Nor would he blame them. He couldn't stop thinking about it. He didn't believe he would ever be able to stop thinking about it. The dead would haunt him, forever. How could a man live with that?
In The Voyage of the Jerle Shannara, Grianne Ohmsford, aka the Ilse Witch touches the Sword of Shannara, which forces her to accept the truth about herself—namely that she's a manipulative, backstabbing bitch who has built her entire life on a lie. She ends up going comatose from the shock, and doesn't recover until near the end of the final book.
Elizabeth Bathory in Count and Countess upon realizing that her closest handmaid has betrayed her and Vlad has stopped writing back to her. Her letters become notably shorter and more frantic before altogether stopping.
Live Action TV
Almost happens to a heartless giant in The Storyteller. The young hero goes on a Fetch Quest to locate the giant's heart (his source of weakness- otherwise, he's invincible). When the hero finds it, he briefly threatens the giant, but decides instead to have mercy and give it to the giant, who already had some Noble Demon qualities, so that he may feel remorse for his evil deeds and change for the better. Then, the hero's less-heroic brother grabs the giant's heart and smashes it.
This is exactly what the Gypsies did to Angel after he killed a daughter of their clan. The curse turned him into the Friendly Neighborhood Vampire he is today. But only after a century of being paralyzed by guilt at all the atrocities he'd committed.
There is also an unintentional example happens at the end of Buffy, season 5. Tearing down the walls between dimensions allows Glory to feel Ben's human emotions, for some reason. She... isn't happy.
It's the tearing down the separation between Glory and Ben that's the problem. He's getting her ruthlessness and self-absorption, she's getting his caring. Neither one is happy about it.
The Mayor suffers a brief one when he finds Faith in a coma.
Mayor: "She's going to be all right. She'll be all right. She'll be all right."
It also leads to the only slip in his polite, Affably Evil demeanor when he runs into Angel and Buffy a few minutes later, he makes some very angry threats and refers to her as Angel's "whore".
Arguably, Sylar in Heroes goes through this in the first-season episode 'The Hard Part.' It doesn't take.
Happens again in Season 4. As of the end of the show, it seems to be taking just fine.
In Ninja Turtles: The Next Mutation, the revealed 5th (and female) turtle named Venus with some rather spiritual abilities, turns Shredder's mind against itself. His suddenly activated conscience angrily wills Shredder into submission and destroys the Foot Clan. This is likely one of the reasons most fans say the series never happened.
Dukat in Star Trek: Deep Space Nine has a particularly bad one while the Federation is retaking the eponymous station. His lieutenant shoots his daughter Ziyal when she admits to helping release a group of terrorists (who happen to be main characters) from prison, and the episode ends with Dukat in a cell huddled in a corner talking to the absent Ziyal, still somehow convinced she is devoted to him.
One episode of House had a patient who was a psychopath. Sociopath. Well, one of those 'paths. She had no problem with cheating on her rich husband (whom she was only using for his money), drugging people to cause them to make themselves look bad, and lying to try to get one of her doctors in deep trouble, among other things. Then they fixed her underlying medical condition and the lack of empathy and conscience wore off, resulting in this trope.
Mr. Wolf, the Anti-Villain leader of a team of hostage-taking bank robbers, has one late in The Kill Point, after his Token Good Teammate goes nuts from a combination of PTSD and gangrene and gets himself shot by the cops.
Dr. Kelso from Scrubs isn't (usually) so much a villain as a boss playing the role of Bad Cop with his underlings, but one episode of Season 5 definitely shows this happening to him. The episode states that it's a well known fact that no matter what happens at the hospital, the second Dr. Kelso leaves the building all his cares vanish. In this particular episode, Kelso promises Dr. Cox to allow Cox' patient (who is a really great guy) a spot for testing a new drug that should save his life. Later, Kelso bumps that patient off the drug trial in favor of a much richer one. Later we learn that Kelso's patient lives while Cox' dies. When Cox angrily confronts him over this, Kelso replies that it was a necessary evil; the rich guy donated a ton of money to the hospital afterward, which allowed Kelso to reopen the pre-natal ward and rehire Elliot. However, when Kelso leaves the hospital that night instead of going straight into being happy and cheerful, he has a moment where he just looks around in heartbreaking sadness. See it for yourself.
In Breaking Bad, Walter White is struck by one in the episode "Ozymandias," following the death of Hank Schrader.
In the final episode of Supernatural's eighth season, Crowley, after having been repeatedly injected with the purified blood of Sam Winchester, breaks down into what appears to be uncontrollable stream-of-consciousness babble ending with a fervent declaration that he deserves to and only wants to be loved. Later in a moment of calm, he sincerely asks Sam where he could even begin to look for forgiveness for all he's done.
One interpretation of Golden Earring's "Twilight Zone" is that it's about a spy-turned-killer having a self-inflicted Villainous BSOD moment.
Seeing clearer what I've done I'd refuse to let things go I could never once admit I'm wrong And what do I have to show? Seeing clearer what's at stake And the things I have to change I just hope I can, it's not too late To get a chance to end this pain
One parody of The Grinch had him die of a heart attack when his heart "grew three sizes too large" after witnessing the Whos' good cheer.
President Eden, the Big Bad of Fallout 3 has a quite literal one of these upon finding out just how insane his plan really is. Eden, being an AI supercomputerdidn't understand he was trying to destroy the very remnants of America he thought he was rebuilding, and as a result either shuts down or self-destructs depending on how the player handles the situation.
Sadly, the dialogue for the final confrontation with Eden wasn't written particularly well, so that unless you look really closely, it just seems like you tell him he sucks and should die, and he just agrees with you for no reason.
The same can be done to the Master in the original Fallout game, in which he will commit suicide if you reveal to him that his plan is doomed to fail, having realized how crazy its plan really was and guilty over what it did in order to undertake it.
This is a possible explanation for how you win the final battle in Earthbound, as well: the prayers of all those you have met overwhelm the ultimate evil within him, and he tears himself apart in realization of what he is.
In Mass Effect, the penultimate boss and Dragon of the first game Saren can be talked into taking his own life when he is forced to understand his plan to help save a fraction of the galaxy is the means by which Big BadSovereign is controlling him. His final words are, "Thank you, Shepard." In addition, Matriarch Benezia heroically gives herself a villainous BSOD during her boss battle. Handwaved as having sealed away some part of her mind.
In Mass Effect 3, you can also talk the Illusive Man into shooting himself by making him realize that he's nothing more than a pawn of the Reapers.
The Secret of Monkey Island: Ghost Pirate LeChuck has a brief one during the ending when he Did Not See That Coming. ( Governor Elaine, whom he was going to marry, is revealed to have escaped and the one in the wedding dress is two monkeys) He just utters lines such as: "Hey...", "What..." "How...". But he recovers quickly.
When you finally catch up with Takahisa Kandori in Shin Megami Tensei: Persona, he's realized that he's gotten everything he's ever wanted and it absolutely sucks. He's demotivated to the point that Nanjo has to needle him about how he's achieved his nigh-godhood through borrowed power in order to prompt the requisite boss fight.
The game You Find Yourself In A Room believes that its hatred and anger toward humanity and torment of yourself as you play is fully justified because it's a superior emotionless being disgusted by the flawed entities that created it. You then get a chance to point out that hatred and anger are actually emotions. This trope results, as it falls into a despair in which it simply lets you go, finding no more meaning to its life.
Golbez fleeing from Cecil after the first fight is heavily implied to be that of a Villainous BSOD (presumably, he retreated out of the shock that Cecil was his younger brother).
Queen Grimhilde (from Snow White) suffers this trope during the battle with her in Disney Villains Revenge, which causes her to destroy the mirror before being killed herself.
Walker in Spec Ops: The Line undergoes one of these when he discovers Konrad has been Dead All Along. What he thought was the real Konrad was an illusion, created by his mind in conflict with itself and acting as a sort of conscience. How Walker reacts to this development depends on the player; he can either commit suicide, or "shoot" the illusion of Konrad and radio for a backup team to continue his original mission of evacuating Dubai. Once they arrive, he can attack them and lose, attack them and win, or lay down his weapon and go home, a broken man.
In A Very Potter Musical, Harry sort of half-heartedly tries this on Voldemort, who almost falls for it. He catches himself in time, though, and Harry kills him the old-fashioned way. He gets better.
On The Spoony Experiment, Dr. Insano had a brief one after creating the Son of Insano, and cried about how his Mad Science never comes out right. His son quickly cheers him up by wanting to help him Take Over the World, ending the moment and turning it into a CMOH.
Mecha-Freeza gets a literal one (we see his point of view, then a few seconds later a BSOD appears on the screen) after Super Saiyan Trunks cuts him in half in Dragon Ball Z Abridged Episode 33. Justified in that he had various cybernetic attachments implanted into his body.
Pre-series, Iroh after the death of Lu Ten and breaking the siege of Ba Sing Se would probably be seen as this by the Earth Kingdom, although he'd apparently been struggling with his father's goals for some time, since he lied about the dragons and had presumably already joined the Order of the White Lotus.
For hundreds of years, Nox from Wakfu has been killing many, many living beings and taking their Wakfu, with the ultimate goal of travelling back in time to see his dead family again, with the side effect of undoing every atrocity he has committed in the name of this goal. In the end, he wins, but all of his accumulated Wakfu is only enough to travel 20 minutes into the past. Hit with the realization of everything he's done, and that it was all for naught, he can only sit still, silently weeping in the wreckage of his Humongous Mecha. The sight of the Big Bad crying silently is unbearable even to Yugo, the hero, who stops the enraged Sadida army from enacting their vengeance. When he recovers, he teleports away to commit suicide on the graves of his family.
In "Judgement Day", it is heavily implied that Two-Face experiences this in his final appearance. He developed a third personality called The Judge, one that even he isn't aware of, and while in Arkham Asylum in the ending of the episode, Two-Face is deliberating in a court in his mind and, while staring blankly, pleads guilty.
In one episode of My Little Pony: Friendship Is Magic, Fluttershy, of all ponies, is charged with the less than enviable task of reforming Discord. Knowing it will be a difficult undertaking, and despite the protestations of her friends, she proceeds to treat Discord with kindness and allows him a measure of free reign with his magic. In return, he pretends to go along with it to manipulate her. At a dinner with the rest of the group, Fluttershy reveals that she's come to see him as a friend, surprising everyone, especially Discord himself. When a calamity of his making arises, she reveals that she knew all along that something like it would happen, and confronts Discord with his bad behavior by stating that they are not friends any longer.