Girl Genius: As the novels explain, Othar's hometown was often ravaged by the mad inventions of the local Spark lords. Then he started to go on his adventures and was proclaimed a hero. Eventually he picked up a Geister that had been abandoned by her sisterhood in the sewers of Paris, with whom he fell in love and got married. They retired to an island for decades and he left only after she passed away from natural causes, to find Europa burned to ashes and everyone and everything was dead save an aged Tarvek. Tarvek managed to send him back to try and save everything, but wasn't able to provide Othar any details because Othar attacked him in a paranoid rage. Othar knows that all of Europa is doomed without his help, but he doesn't know what needs to change. All he knows is that sparks will cause the Bad Future, not why or how, so he kills all sparks he comes across on the chance that they have something to do with causing Europa's destruction either directly or by being a Spanner in the Works. The problem is that he's so insane that he can't sort out who is aiding the Other directly or indirectly.
Lord Tedd may or may not have one. Consider the facts that he is the most powerful known being in the comic and that the creator admitted that people wouldn't like his backstory because it is just that sad. The adults in the prime universe (which is a decade or so behind Lord Tedd's) seem to believe he has one though, and are going to a lot of effort to make sure their Tedd doesn't suffer the same fate. For example, Raven is reluctantly willing to take Grace on a hunt for a dangerous boar...until he finds out she's Tedd's girlfriend, at which point he freaks out, and only agrees to take her under extreme duress.
Raven: You will follow my orders without question. If there is danger, you will leave me to die. Do I make myself clear? Grace: But— Raven:Do I make myself clear?
Susan also had a couple of events that shaped how she was now. The event that shaped her Straw Feminist views on men was she catching her father with a naked women who was not her mother, and her mother being a Straw Feminist herself, this is also the reason why she dyes her hair dark-blue. She also used to be a literal Wide-Eyed Idealist before her trip to France where she and Nanase were hunted by a vampire-like Abberation, and Susan being forced to kill it. Thankfully after a couple of arcs, she has gotten some closure and a less strained attitude.
In Fans!, Alisin Oberf, during her dark days when she was dying of a rare disease, was, beneath her Perky Gothexterior, a self-loathing mess, who took pleasure in heavy bondage and sadism. Years later, after she was cured of the disease, but not her negative self-image, one of her "partners", Keith Feddyg, emerged as Alisin's greatest nemesis, using her own self-loathing to force her to become his sex slave and blaming her for his having become a psycho. Subsequent evidence indicates that he was alreadythere before Aly ever showed up.
Also, Alisin killed Robert's goldfish, which may or may not have something to do with the latter's eventual world dominating ambitions.
Joel Calley from Concession has about three Freudian Excuses: his father left their company to his older brother Julian, his sister Miranda was killed by Julian when they were young, and their parents blamed Joel for the murder and put him in an asylum where he was sexually abused by a doctor. There have also been a couple of throwaway gags which, if taken too seriously, could imply that his mother resents him for not being a girl. If there was a trope for Freudian Sue, Joel would probably be the poster boy. However, much of, if not all of this is ultimately subverted when it's later revealed that Miranda actually died in her sleep and that demonic Miranda encouraged Joel to do bad things so she could feed on their suffering. It must be noted Joel willingly helped her and was already sadistic. When confronted about this, Joel immediately notes that his and Miranda's real motives are to gain power. In the end, Joel's only real excuse for his actions is that he's a goddamn psychopath.
Token Evil Teammate Belkar spins a sob story about being mocked as a child and becoming an adventurer to get strong enough to take revenge. However, he only says this to get free experience points for proper role-playing.
Played straight with Redcloak, who lost his village to the crusading of the Sapphire Guard as a child.
Might also count for Nale, Elan's evil twin and The Unfavorite to their father, General Tarquin. He's evil, but incompetent because of ego. What he wants nothing more is to be his own man, and step out of his father's shadow and manipulation. Tarquin agrees to this, since it was the only thing stopping him from avenging Malack.
Subverted in Start of Darkness with Xykon. The opening scene has a child who will grow up to be Xykon crying over his recently deceased dog, Barky. He spontaneously reanimates it as a zombie. When the Barky attacks a bird and eats its brain, child!Xykon decides it's awesome and runs off to find more small animals for Barky to savage. Apparently, having a savage, gory murder machine is a lot more fun that whatever kind of dog Barky was in life.
For roughly the first four years of the strip, Kell Dewclaw's brother, Ralph, constantly tried to hunt and eat his brother-in-law, Kevin. It initially wasn't explained why he was doing this, nor why he was so inept at hunting. Eventually, Kevin taught him to be a coder, and later hired Ralph to Hare-Link, warming the relationship. The reason was subsequently revealed when Corrie was identified as Ralph's daughter: he had carried out a romance with Wanda Woolstone, a sheep. She got pregnant, and died in childbirth. He tried to hunt Kevin because he didn't want Kell to be hurt should she lose Kevin, but by that time he was too out-of-practice to accomplish it.
Desdemona Fuscus tried to push Lindesfarne and Fenton to marry earlier and earlier. This was because she was secretly a vampire bat, and didn't want Lindesfarne to find out and call off the wedding.
Carl resisted Leona Mangle's Rescue Romance advances because she had tried briefly to hunt one of his friends, Miranda Hutch, after she broke up Leona's relationship with Edgar Carnassial in an affair. Carl later accepted Leona when Miranda spoke up in her defense, as the two had subsequently come to an understanding.
Related to this, Leona would later reveal that she was attracted to Carl because he reminded her of a unicorn. But she closed herself off after a petty issue because of the death of her mother when she was a child; she tended to run from relationships at the first sign of trouble, so they wouldn't disappear like a unicorn...or her mother.
Ménage à 3: The characters from this comic mentioned below aren't actual paid-up villains, but they still have excuses.
Gary's virginity and sexual dysfunction are allegedly a result of his severely repressive ultra-religious parents, plus cockteasing girls in his teen years. (And he lives with two women who engage in a lot of sexual teasing, albeit mostly by accident, and lusts after a girl with penis-phobia. Um...) However, this has never been mentioned again since the early strips in which Gary told the story, and the writers may not consider it very important; Gary's problems don't need that much explanation — he's just a hopeless geek, with his geekiness Turned Up to Eleven. And when his mother 'phones to wish him a happy birthday, she sounds nice enough.
The root causes of Kiley's runaway A-Cup Angst are apparently finally revealed in strip #916 (August 07, 2014, NSFW). They go back to her teenage years.
Off-White: She's not a villain, but the tragic death of most of her litter is at least partly to blame for Jera's attitude.
Vriska from Homestuck is partially a HUGE BITCH BLUH BLUH because her guardian was a giant spider to whom she had to regularly feed other young trolls or be eaten herself.
Drowtales: Ariel, the 'main character' of the story. The first 10 years of life were dominated by an sociopathic stepmother who envied her own child. And then forced by her high-standards grandmother to murder some punk who tried to kill her. And finally realizing that living up to her grandmother's standards caused her to fail in protecting her best friend. By the time she's done with all that, she lashes out at one of her friends and ends up killing an innocent in the crossfire. Once this happens she has a My God, What Have I Done? realization and moves off the Villain Protagonist path to a more heroic one.
Also claimed by Snadhya'rune, who is effectively the Big Bad, who says that the pressure her mother the Empress put on her and the death/posession of her "twin" Khaless made her crack and eventually murder her own mother. It's suggested in story this is bullshit and she's actually a straight up sociopath, though.
Snadhya's daughter Kalki, on the other hand, may have a genuine one since her mother passed her off to servants and never showed her affection, making Kalki a desperate Attention Whore who feared she would be replaced, fears that were founded when Snadhya killed her in cold blood saying she was nothing but a tool.
Jamie from Khaos Komix is a foul-mouthed homophobe who bullies Alex for supposedly being gay and disowns his best friends after they come out to him as a gay couple. Then you learn that he was sexually abused as a child and has a mother who doused him in scalding water when she caught him Playing Doctor with another boy which has led to him having massive issues about sex and sexuality and you wonder why he isn't even more messed up. However, he actually criticizes the use of this trope by stating that he doesn't believe that his traumatic past excuses his actions and that he still has to work hard to redeem himself.
In Freefall, Edge spent his formative years in a warehouse surrounded by unintelligent machinery. Robots using Dr. Bowman's Artificial Intelligence architecture, like humans, need proper socialization, and he's turned out with an It's All About Me attitude and the complete conviction that he's always the smartest (and most important) person about.
Sticky Dilly Buns has Ruby, who was traumatized at the age of about 14 when she discovered that her sister Amber was a porn actress - by being exposed to one of Amber's videos at a teenage party. Okay, that involved her sister rather than her parents - but the problem seems to have been compounded by having to keep Amber's secret from their parents for the next several years. Fortunately, her "villainy" is limited to a fear of men and a petulant attitude towards Amber, but it makes her hard for Amber to live with.
The Bedfellows strip where Sheen starts seeing a shrink reveals that his bad attitude can be traced back to when he was heckled out of a kindergarten play. The hecklers? His parents!
Played for Laughs in Axe Cop — a comic where bad guys are usually Card Carrying Villains doing it For the Evulz — in the story "The Songster". The Torture Master is first introduced as a total villain, but then the Songster starts singing about his tortured past... which contains incidents that happen to everyone. (At most he might have been a Butt-Monkey.) So it was things like unrequited love in college and losing in tic-tac-toe that made the Torture Master start tormenting people to death by enacting their worst fears. Then things get completely out of hand as the Songster's lyrics about how "that's how a monster is made" turn literal, and he uses his song to turn the Torture Master's past into the ultimate monster: a mouse that sends you to Mars when you look at it.
In the same story, the Songster became a villain because he thought that the heroes had killed his parents... but when he finds out it wasn't true, he decides to continue being a bad guy anyway because he kind of likes it.
I'm the Grim Reaper: Ana, the woman who killed her son, is given one: she had parents that squashed her unconventional dreams of becoming a writer, and pressured her into getting an ordinary life by marrying an ordinary man, who abandoned her shortly after she had their son. When her son became terminally ill and she didnt have the funds to get medicine, she killed him. However, it is presented as less of an excuse, and more of an explanation, especially since while Scarlet feels sorry for her, Chase has no sympathy, saying there's many things she could've done to get money before resorting to murder.
One-Punch Man: As a child, Garou was bullied and forced to play the monster to please the popular kids, which made him empathize with monsters who were hated by everyone and always got defeated by the hero. This belief gradually took an extreme turn and made him want to become a monster just to defeat the ever popular heroes.
Jagganoth was a Child Soldier drafted into a mercenary outfit called the Corpse Legion at a young age after they destroyed his hometown and killed his family. He was subjected to intense Dehumanization of the self, to the point that he lost his original name and became only a "Dead Man" fit for killing; by the time the Universal War wound down he had become a Shell-Shocked Veteran. Lacking any other meaning in life without war, he became convinced by an angel that the best thing to do was to save anyone else from his suffering by annihilating the multiverse.