In the last case of the second game, Justice For All, it is revealed that the client is indirectly guilty of the murder, having hired a hitman to do it for him. After proving his guilt, the player (Phoenix) gets to decide the guilty man's fate. Have him declared "Guilty" where he will go to jail, or let him be "Not Guilty" where he will immediately be targeted by the hitman that he tried to use as a scapegoat. It's such a lose-lose situation for him that if you choose "Not Guilty," he'll beg and scream and confess to everything just to get the extra buffer of prison security between him and the hitman.
In Trials and Tribulations: Dahlia believes that being dead makes her beyond punishment by the living. But when Phoenix reveals that the target of her revenge, missing and presumed dead, is in fact the medium whose body she is currently inhabiting, he and Mia explain in detail how each of her crimes was a failure, and that she has doomed herself to the "ultimate punishment": spending all eternity as a miserable, pathetic loser. In hell.
Happens to the killer of Case 2 of Dual Destinies. Florent L'Belle, after his Villainous Breakdown leads to him losing his hair dye and make-up, is revealed as a haggard middle-aged man. He then answers a series of calls on his cell-phone epaulets, learning that his sponsors are leaving him, he's being fired as the mayor's aide, a vague project is being cancelled, and he is being sued for 100 million dollars for damaging the stratosphere with his products.
Some of the deaths of Roger Wilco involve him getting (even posthumously) humiliated, such as the Two Guys from Andromeda barging in to show a replay of him purposefully inhaling acidic gas, or an alien couple mistaking Roger's pod disintegrating in the atmosphere for a shooting star, and having a discussion that concludes that "there is no intelligent life in space".
Suikoden IV has Snowe suffer through a conga that lasts almost the entire game. The start of the game paints him as a daddy's boy and a Dirty Coward that only got to where he is by nepotism. In time, he sells out his own countrymen to avoid having to fight, and tries acting like a "wound" on his arm kept him from helping anyone in an ensuing battle. In truth, he just turned tail and fled. He manages to get away, but runs into the Player Character several more times throughout the game. Each time Snowe is encountered, he's become more of a Jerk Ass and more increasingly pathetic as it becomes clear that the player is helping far more than Snowe is. The player does have the option to kill Snowe a few of those times, but letting him live seems more like Cruel Mercy. But, if the player keeps letting Snowe go, then by the end of the game, he's eaten a huge slice of Humble Pie and finally sees the error of his ways. Having him in the player's party also unlocks a Game-Breaker double team move with Snowe and the player, so it might be worth sparing his sorry hide just for that.
In Suikoden V: Lord Barows suffers one of these when his schemes are revealed. After a particular battle, his secret allies from an enemy nation think he betrayed them; everyone in the party (and anyone in the world who cares to think about it) now knows he is a traitor and is secretly laughing at him as he stammers humiliatingly transparent congratulations. Then his son bursts in and demands that he use the missing MacGuffin whose theft helped spark the current war, revealing that his father was responsible. Then his daughter betrays him and helps the heroes recover the item, which instantly bonds to the hero despite two years of failed efforts to control it by Barows himself. Then everyone goes from laughing secretly at him to laughing openly at him; all his former allies, one by one, tell him how awful he is and abandon him; his daughter leaves to join the hero, telling her father she hopes she never sees him again; the hero's strategist gives one last parting shot... and then the last person in his manor, his Gentle Giantstorage-room guy, runs out at the last minute to abandon him and join the heroes as well. Oh, and his end was really painful too: Sialeeds kills him, and as he is in his dying breath, she told him that with the patheticness of his son, his family is just about ready to plummet into destruction.
In the first Drakengard game, a really brutal Humiliation Conga is served to Manah in the first ending (the one with the least tragedy, to be clear). When the Big Bad goes as far as to beg the Anti-Hero to kill her, or else she will... do something, you know she has hit rock bottom.
Melodia from Baten Kaitos also qualifies. Her plan to resurrect the dead god and become the ruler of the new world fails when the heroes defeat it. Then, her grandfather tells her that she has been manipulated by the said god all along as part of its Evil Plan. She doesn't take this very well and fuses with the dead god. However, when the dead god is finally destroyed, she ends up getting rescued by the hero. While she is not present in the ending, it's implied that she is suffering due to the massive amount of guilt over almost causing the end of the world.
In a heroic (at the time, anyway) example, Oersted of Live A Live gets put through one of these in his chapter, courtesy of his childhood friend / Unknown Rival Straybow. To explain the whole thing would make this entry waaaaaayyyy too long, so to summarize it:
Princess gets kidnapped, Oersted goes off to save the princess, fails, gets tricked into killing the king, goes back to confront the evil demon and try to save the princess again, finds out that Straybow orchestrated the whole thing 'cause he wanted to humiliate Oersted, Oersted kicks his ass, princess more or less walks in, declares her love for Straybow, and then kills herself.
Oh, and we forgot that he also watches the great hero of the land die, helpless to assist him, and than, he witnesses the hero's right-hand assistant die right next to him as well; by the end, everyone who said they believed in him dies. Let's just say, he doesn't take it well...
A tad more understandable, when you think about the fact that everyone in the kingdom declared that he was the demon when he accidentally killed the king. They tortured the other hero, the one who believed in him, almost to death. They drove him from his home, but Oersted still clung to the words "As long as there is still one person who believes in you." The princess's trust in him was his last hope. And then, well...
In Road Runner's Death Valley Rally, Wile E.'s signature traps (including the batsuit, explosives in model airplanes, and catapults) repeatedly backfire on him throughout the game. At the end of every "boss level," though, he really gets it, yet he keeps shooing away the fat lady who would end it all by singing. Culminated in the final level, when the Road Runner destroys the Coyote's Humongous Mecha. Since said battle occurred on the moon, you're treated to the usual "Coyote plummets towards the ground" shot... except he's plummeting towards Earth from orbit. On the way down, he holds up a sign requesting that the game end before he hits. It doesn't. Instead, he lands neck deep in the ground, scant feet from the finish line to the titular race. Then, a truck runs over him, dislodging its cargo of exploding planes and robots. Which naturally all converge on him and explode. The Road Runner then runs up, gives the raspberry, and crosses the finish line. Then, the fat lady is heard singing... and a Shadow of Impending Doom appears over the Coyote. It ends much as you'd expect.
In Assassin's Creed: Brotherhood, Sequences 5 through 9 are one long spree of failures for Cesare Borgia: first Ezio murders Cesare's money-man who was his main source of funds, then he deprives Cesare of his French allies and (optionally) his Leonardo da Vinci-designed war machines, kills Cesare's lieutenants, and wrests control of Rome away from Cesare, all right under his nose. Cesare then gets a stern talking-to — and attempted poisoning — from his daddy, who'd withheld financial support for him and didn't even tell him about the death of his French general, though Rodrigo's attempt at a last solution fatally backfires. Cesare's own sister Lucrezia betrays the location of the Apple of Eden to Ezio, who reaches it first despite Cesare's head start, and then wields it to escape from the Vaticano District, incapacitating quite a few Borgia troops along the way. Several surviving Cardinals put their support behind "Della Rovere" (actually Giuliano della Rovere) for the Papacy after telling Cesare that his family's money is "tainted," even though Cesare had paid for their appointments. After several skirmishes in Roman streets are all lost by Cesare's men, in the final battle for Rome, the Assassins openly take to the streets and literally force him outside one of the city gates. Even then, Cesare still believes that his army is returning to retake Rome, led by his hitman... but instead, a general forced into his service arrests Cesare at the new Pope's order — complete with a charge of incest — and Cesare is dragged away by Papal Guards who he might have previously commanded. It would be a year or more before he escaped, breaking several bones in the process, and Ezio would finally catch up to him while Cesare was making a last desperate grab at a comeback — not commanding, but commanded by a relative.
So far in AdventureQuest Worlds, no villain has actually died, they've just been defeated and left with humiliatingly unpleasant fates.
Escherion turned himself into a frog after his powers got inverted by the hero due to his magic being reflected back at him.
Vath was carried off to an unknown fate by Stalagbite after the hero destroyed the false Dragon Amulet that he had been using to control him.
Kitsune got sealed into a rift leading him back to the Yokai world after the Hanzamune sword was recovered by the hero.
Wolfwing was reduced to a pile of dust by an arrow fired by Shadowslayer Z (though the Mystic Wolf Moon began slowly restoring his remains).
Discordia was unmasked and revealed to be a fake Chaos Lord controlled by the real Chaos Lord, Kimberly, who eventually had the Chaos Ear Worm in the form of a Chaotic song sung to her by Drakath that got stuck in her head beaten out of her, returning her to normal and causing her to join the heroes' cause.
Ledgermayne was converted by the Supreme Arcane Staff (and Drakath's power) back into the raw mana from which it was made.
Maximilian Lionfang was captured after trying to destroy Frostval and remanded to Swordhaven's dungeon.
Tibicenas was stripped of all his Djinn power by the leader of all Djinn, the Efreet, before what was left of him was destroyed by the hero.
But probably the grandest Conga to date has to go to Noxus at the end of the Shadowfall War. After Vordred is called away by Sally just as he and Noxus are about to finish the heroes off with Gravelyn's own undead army, which Noxus himself first created for her father Sepulchure, Noxus gets knocked right off the Shadowscythe throne by Chuckles, the skeletal minion who was killed by Drakath on his first appearance and is now nothing more than a skull. Chuckles was unaffected by the spell that turned all of Gravelyn's army against her because Noxus didn't create him — he was Gravelyn's first undead minion. Chuckles frees Gravelyn, who wastes no time in taking back control of her army and allowing the heroes through to defeat Noxus. After Noxus is defeated, he gets blasted one in the face by Gravelyn herself when he taunts you on how he cannot be killed. As the Hero and Gravelyn talk about Vordred and the upcoming Arc Attack event, the Hero smacks Noxus down each time he tries to rise again, until Gravelyn gets the idea to give Chuckles a promotion — by swapping his skull with that of Noxus, giving him a new body! Gravelyn promptly delivers a Shout-Out to Hamlet with Noxus' skull, before planning to have it made into a new weapon for her... by Cysero. Tough break, bonehead!
In the Redemption mod for Baldur's Gate IIThrone of Baal, Jon Irenicus goes through one as part of his redemption. Forced to live through the pain of all of his victims in an instant, he is left in the body of a teenager with a fresh soul and nearly all of his magic forgotten and lost. His epilogue isn't any gentler on him: he suffers insomnia, gets sold into slavery, and realizes that he can never go back to his homeland even after being given his second chance — he has changed too much. On a more hopeful note, he becomes a better and gentler person, reluctant to use his magic to hurt anyone ever again.
Oddly enough, Grolla Seyfarth in RosenkreuzStilette has to go through a Conga as well, giving her side-game a Downer Beginning. Despite being of a Badass Family who's wielded an Ancestral Weapon for generations, she gets humiliated by the Magnificent Bastard Iris, who first shows off her badass power by attacking and heavily injuring her with a sphere attack and then pulls off a Wounded Gazelle Gambit, making it look like she's an innocent girl being threatened when Sichte walks in, causing her to order Grolla to lower her weapon. But knowing that doing as Sichte ordered could end up causing her own life to be forfeit, Grolla ends up retreating as a result of the humiliation. Tough luck, descendant of Seyfarth!
Donkey Kong 64: In a five-part final boss fight, K. Rool is not only beaten, he's outright humbled. Highlights include Diddy Kong dropping arena lights onto his head, Tiny Kong shooting him in the foot with arrows sixteen times, and Chunky Kong growing to K. Rool's size and punching him into next week. After it's all said and done, Funky Kong shoots K. Rool in the ass with a rocket launcher, blasting him to the lair of a giant minion he betrayed, who pummels him even more. That'll teach him to try to blow up DK Isles!
Mass Effect 2 can be seen as one for Harbinger, as he goes to great lengths to kill Commander Shepard, then hires the Shadow Broker to make sure s/he's dead; the Broker fails to get Shepard's body and Shepard is rebuilt, tougher and better. Then goes on a Suicide Mission, which Shepard survives, killing Harbinger's most useful minions as well as a potential ace up the sleeve (the human reaper). After which, Shepard kills the now Reaper-allied Shadow Broker, replacing him with a good friend. Then when some of Harbinger's indoctrinated humans capture Shepard and stop him/her from destroying the Mass Relay the Reapers would use to easily travel all over the galaxy, Shepard escapes, kills everyone in his/herway in the entire base, and destroys the aforementioned Mass Relay. It culminates when Harbinger uses a hologram to talk with Shepard, in which he says:
Asura's Wrath: Near the last leg of the final battle, Chakravartin the Creator sports his own Sanskrit lettered Action Commands. But after getting hit repeatedly by Asura's barrage, he physically staggers and the action commands start to fail. Asura is just casually pummeling him and countering his attempts to fight back at this point, giving a rather epic and angry speech how he's not going to take any more shit from anyone that calls himself a god and/or makes his daughter cry. So he takes quite a beating before finally dying.
Adachi in Persona 4. When you finally catch up to him, he finally explains himself and his justification... which leads to the entire cast pointing out that he's nothing more than a child in a man's body who can't deal with his own failures and blames other people for his own shortcomings to the point of self-loathing. There's no fear of him anymore; they just want to take him in and get the pest out of their hair. After being beaten by a group of high schoolers, including the cousin of a girl that he tricked someone else into trying to kill, he just ends up becoming a puppet for a greater entity and finds out that he was ultimately just a pawn. By the end, he's broken and admits to everything he did in a more believable way than the actual truth, finally accepting what a terrible human being he is for the first time ever.
In Twisted Metal: Head On, Calypso ends up having to grant a wish to Sweet Tooth, who he insults as usual. It is at this point that Sweet Tooth starts to think; why is he doing all the dirty work for nothing but a wish that will just bite him in the ass anyways? Why not be the guy calling the shots, with the hot women around him on a throne and a squad of armed guards, all while tricking people into mass slaughter for kicks? So, he decides that his wish is to 'Take Calypso's place', which Calypso has no choice but to grant because of the way his power works. He ends up in Sweet Tooth's body and the now-in-charge Needles Kane tells his guards to gun the guy down. Granted, you had the ending with Minion in Twisted Metal 2 where he was dragged to Hell, but this particular case just screams twisted irony.
Mario Kart: You think you've secured first? Cue Spiny Shell, Lightning, POW Block, Bob-Omb, and a Blooper for good measure. And, with your luck, this happened halfway through the last lap.
GLaDOS in Portal 2 goes through a series of this, although she probably deserved it after trying so damn hard to kill you in the first game and the second game. After being destroyed by Chell previously, GLaDOS, after being revived, tells Chell how she had to endure reliving her death over and over again for years (implied to be hundreds or even thousands of years) because of her black box quick save feature. After GLaDOS decides to try and kill Chell again, she discovers that Chell replaced the turrets with crappy ones and disabled the neurotoxins, making GLaDOS helpless. After that, Chell forces a process that swaps GLaDOS and Wheatley's bodies, to which Wheatley stuffs GLaDOS in a potato and after that, she gets partially eaten by a bird.
XCOM: Enemy Unknown: MutonBerserkers, when wounded, will roar and charge straight at the soldier who shot it. Set it up just right, and brace yourself for major lulz as the Berserker runs all over the map getting shot over and over by your troops, who are probably wetting their Titan armor from their laughter.
Thanks to some Video Game Cruelty Potential, you can put Captain Hook through one in Kingdom Hearts I. Not only is the player required to beat him up, after Peter had poked him in the rear with his dagger, but you can amuse yourself more by making Captain Hook jump off the ship (or throw him off!), causing him to yell "YOU'LL NOT GET ME OTHER HAND!", or light him on fire with Fira. Then after he is beaten, the crocodile starts chasing after him. And if you carry a lot of status-inducing spells in Kingdom Hearts: Birth by Sleep, you can make Captain Hook's day absolutely miserable — he's only immune to one status effect. Suddenly, his status as That One Boss in Chain of Memories makes sense — he wants revenge for the torment you likely put him through.