Drow Tales. Sarv'swati Vel'Sharen watched her rule crumple around her. Her hold on the city of Chel toppled before her eyes, as the Val'Sarghress rushed through her streets, killing her army and children and pressing ever close to the total destruction of her line. She started slipping deeper and deeper into desperation, her soldiers conducting more guerrilla tactics and Sarv'swati eventually hiring an entire army of raiders, allowing them to enslave and raid her city in return for their services. As she faces her final defeat at the hands of the Sarg's and is forced to flee to the site of her mother's murder at her hands, she breaks down, screaming in horror and curling up to say how sorry she is and how she wishes her mother would come back. Sarv'swati is a centuries old ruthless dictator, now begging for her mommy.
In the Sluggy Freelance story arc "That Which Redeems", Horribus becomes increasingly obsessed with catching Torg as the story progresses, to the point of jeopardizing his invasion of another world. By the end of the story, Horribus is curled up in the fetal position, gibbering about how Torg's behind everything wrong in his life.
In It's Walky!, Sal has a series of these after the appointment of Linda Walkerton as the head of SEMME drives her to make a Face-Heel Turn. This culminates in what amounts to a Villainous BSOD when her attempt to blow up the world using the Power Booster Rod is interrupted by the arrival of Danny, the only person left that she has enough feelings for to not be psychotic enough to kill. Prior to that, Sal's Villainous Breakdowns tended to not immediatly proceed her capture because she is super-strong, and so even thrashing about in a blind rage, she tends to beat people.
Dr Merlot seemed to take news of Miss Clay's true identity rather badly.
While his breakdown was just very hammy, Zola suffers the most dangerous variation. After she forfeits her chance to escape for another attempt to kill Agatha and fails, she takes a beating and it looks like she will be defeated rather anticlimatically. Then she decides that it is better to die with her foes than to lose, downs a vial of Psycho Serum and goes on a murderous rampage.
Damien of El Goonish Shive has an absolutely EPIC breakdown when, during his battle with Omega Grace, he realizes that he was very likely created in a lab like Grace and her "brothers" (as opposed to his initial belief that he was a god that was summoned to this world), and ends up self-destructing in an attempt to kill Grace.
Even more epic since he saw this as a twisted win/win. If he was a god, he would survive. If he wasn't, he didn't want to.
Start of Darkness spoiler: Xykon, also loses it shortly after turning into a lich, when he realizes that he can't taste coffee anymore.
Tarquin begins to lose it when seeing that his son Elan is quite happy being the support for his team instead of trying to be the leader. And just in general for being treated as some second-rate Arc Villain when he believes himself to be the Big Bad, refusing to admit that that particular title belongs to Xykon.
Tarquin: (to the Order at large) What the hell is wrong with you? How did you all get to such a high level without anyone teaching you your place?
After that, he only continues to further lose his cool, threatening to kill absolutely everyone Elan knows and cut off his hand, right until he's given a short talk while hanging off an airship, and left to drop into the desert. He survives the fall physically, but mentally might be another matter...
Elan, this isn't over yet! Where's the growth? You didn't lose anything! Nothing has changed! ELAN, YOU COME BACK HERE AND GIVE THIS PLOTLINE A SATISFYING RESOLUTION THIS INSTANT!!
....ELAN! THERE'S NO SENSE OF CLOSURE! I DON'T KNOW WHAT HAPPENS NEXT!
THIS IS A TERRIBLE ENDING!!!
There are at least two characters from Kid Radd who seem to be likely candidates for this treatment, but the ultimate breakdown goes to somebody else. The Seer does not take holes in its omniscience very well. Not well at all.
In The Inexplicable Adventures of Bob!, the first time Bob beats Fructose Riboflavin, Riboflavin is disappointed but takes the defeat fairly gracefully. The second time, though, he collapses in tears, sobbing that he's been trying to conquer the Empire for centuries and he just can't do it— and Bob proves himself a nice guy by trying to cheer the villain up.
Bonnie: WAIT ONE GODDAMN SECOND, YOU CUNTS! I DID NOT DO THIS FUCKING FAKE ACT FOR 39 DAYS JUST TO GET FUCKED OVER BY A JURY FULL OF GODDAMN BITTER BITCHES! I WAS THE ONLY PERSON PLAYING THIS FUCKING GAME ALL SEASON! AND I BETTER GET MY GODDAMN MONEY! I CONTROLLED FUCKING EVERYONE! I WAS THE MASTERMIND! I DID EVERYTHING! THIS WAS ALL ME; YOU BETTER GIVE ME WHAT I FUCKING DESERVE!
Jeff Probst: Well, I'm glad you think that. Because the jury seems very eager to ask you some questions.
After awhile in 8-Bit Theater, Sarda gets tired of the games and decides to just outright torment the Light Warriors until the end of time, made worse by absorbing Black Mage's evil side.And then came Chaos...