The Golden Age Arc, which is canonically the third Arc in the manga but the first chronologically, serves as one for Griffith, who was previously seen once as Femto right before the arc started, and explains Anti-Hero Guts's motivations.
Dragon Ball Super: Zamasu. While he never trusted or liked mortals, he wasn't actively against them or wanted to kill them. He just wanted to take a more direct approach when dealing with mortals who abused the gods' knowledge, instead of just watching and guiding. Things, however, went downhill the moment Present Zamasu meets Goku. Not only is Goku a mortal who is friendly with gods, but he is also more powerful than most gods outside of the Gods of Destruction. Once Zamasu gets into his mind that mortals are stupid and dangerous, everything else was confirmed bias.
In chapter 436, we are given a look into Zeref's past, including the source of his "Instant Death" Radius. He was cursed by a god for trying to bring his dead little brother back to life. However, this was only the beginning. Later on, Mavis reveals when Zeref truly fell into the darkness: he fell in love with Mavis after he found out she had the same curse and she proposed that they give Eternal Love a shot. However, their first and only kiss kills her because his love for her is strong enough to empower his curse to take her supposedly immortal life. To have the only person who ever brought him happiness be so cruelly ripped away is what would finally break Zeref and cause a downward spiral that he would never get out of.
The anime gives some Adaptation Expansion to Acnologia's backstory to explain his descent into villainy. He was once a human doctor in a city where dragons and humans coexisted, and took his name from the leader of the city's dragons. The original Acnologia ultimately massacred the city's humans (having grown disillusioned with humanity when he encountered Dragon Slaying magic), triggering the human doctor's hatred of dragons and quest to exterminate them, which in turn, thanks to He Who Fights Monsters, transformed him into an Ax-CrazyOmnicidal Maniac.
Fate/Zero is a story that's just as much about Kiritsugu Emiya destroying himself as Kotomine Kirei turning into full-blown villainy. Despite a lifetime of priesthood, Kirei never found happiness without the suffering of others, and is painfully aware of it. Enter Gilgamesh, who gradually convinces him to embrace his true nature as a sadist.
Future Diary: Yuki used to be a sweet, shy boy living an unextraordinary life. However, once he obtains his Future Diary and meets Yuno, that sweet boy becomes a faded memory, especially after his mother dies. His morality begins to disappear as the show progresses and he comes to love the girl who has stalked him and killed several people. Meanwhile, Yuno herself is given this treatment later in the series when her Dark and Troubled Past is revealed to explain her Ax-CrazyYandere behavior. Specifically, it's revealed that the Yuno Yuki has known during the series is actually a version of her from an alternate timeline. In that timeline, Yuno was left severely traumatized after accidentally killing her Abusive Parents, causing her to become fixated on Yuki after he extends some innocuous kindness towards her. Yuki then dies during Deus Ex Machina's contest, which she wins, becoming the new god of reality. This proves to be her Despair Event Horizon, and she, having lost whatever sanity she had left, restarts the timeline to go through the contest with Yuki again.
Guilty Crown: In episode 15, Shu of all people has one of these. Hare is killed right in front of him (in his arms) because of something stupid and selfish done by Souta and his friends in order to prevent the creation of the Void Ranking System. After her death Shu gets Dull Eyes of Unhappiness and mounts Inori and forcibly removes her Void and procedes to chillingly emotionlessly systemetically rip to pieces the mechs attacking them. He then proceeds to go hysterical and begin pounding Souta's face in before being dragged off by Yahiro. His next words hit the characters (and the audience) pretty hard:
Shu: "I was wrong. Kindness is pointless. We have to separate the good from the trash. I'm going to become king." Heil Mein Shurer.
In Hellsing Ultimate it reveals that Alucard was raped by the Turks when they invaded his nation. While that didn't break him, it can be considered the first step in his path to becoming the ultimate vampire and most powerful being in this series as well as completely mad and battle-thirsty.
Another point could be how he became a vampire. Having waged war on the Ottoman Empire and having sacrificed everything, including his people and subjects for the glory and promise God would save them, he was captured and to be executed. Feeling betrayed, dark forces offered him power and by taking in blood, he turned his back on god and he became a vampire.
A series of flashbacks taking place prior to the events of Stone Ocean act as this for Enrico Pucci and Weather Report. Specifically, the death of Perla Pucci was this, as her death caused the former to become the Well-IntentionedKnight Templar he is now, while the latter gained his hatred for humanity from the event.
While the manga goes with the idea that Dio Brando was born evil, the Over Heaven spin-off novel (a defictionalization of DIO's journal from Stone Ocean) goes into detail on his past and what made him who he is when the series starts. In the novel, Dio himself specifically sees the death of his mother as this, as it was her being worked to an early grave despite her kindness that led Dio to the conclusion that Virtue Is Weakness. Had she lived, Dio most likely wouldn't have become the vicious monster he is now.
Mazinger Z: Dr. Hell's mind was already unstable and unsound due to his upbringing (he was abused by everybody when he was young, including his parents — particularly his mother, who often said she never wanted children and would be better off without him, and was not above hitting him for no reason). However, when he found out the woman he loved was in love with another man Juzo Kabuto, future builder of Mazinger-Z and Kouji's grandfather, he... flipped out and attempted to murder his perceived rival. Shortly after he tried helping someone... and he got the crap beaten out of him for it. Later he crawled back towards his home, bruised and blood-stained, muttering "Mediocre imbeciles! You don't deserve to be alive! One day I'll purge the world of all of you! And then everybody will kneel before me". When you heard his words and saw his utterly mad stare you realized he had snapped out completely and Dr. Hell had been born.
Let's say people had shunned him out of scorn before, but after that point they did it out of FEAR.
Naruto has done this with many antagonists so far, and attempts to justify the Uchiha examples, by claiming that their powers take hold of them because they love too much:
Deuteragonist Sasuke Uchiha witnessed his brother Itachi murder their parents, after murdering their entire clan. He then was subject to days of Mind Rape compressed into seconds, and a challenge to kill his brother when he's ready. None of this makes him "evil", so much as focused on killing his brother, a world-class criminal, on his own, having gone from a frendly outgoing boy to a brooding young man. He does start recovering when he meets up with Team 7, but his second encounter with Itachi not only undoes all the recovery he has been going through, but deal further damage to his sanity and doubts, leading him to fight his rival and protagonist Naruto out of fear he will be surpassed. This fragile state of mind means he's vulnerable to temptation; he then follows Orochimaru, the series' first Big Bad, to gain the power to beat Itachi. After the Time Skip and having become a colder person, he does finally defeat his brother... until the mysterious Tobi decides to reveal some secrets. He tells Sasuke the truth about Itachi's backstory, that the clan itself was planning something and Itachi was just following orders, he becomes seriously mentally imbalanced and unstable, playing into the hands of the new Big Bad manipulating him, Tobi, and he decides his best option is revenge on their entire home town. Only after learning more about everything, defeating the final Big Bad and one last battle with Naruto does he finally reach his end of the darkness.
Gaara grew up believing his mother named him as a curse against everyone else, for her having to die in childbirth. His father had warriors and himself to keep Gaara in line, because of the demon sealed within him, which would be unleashed if he lost control of his emotions or even slept. As a small child, he believed that there was only one person who loved him, his maternal uncle Yashamaru. The betrayal of Yashamaru transformed him from an attention-starved waif to a serial killer. He came around to the side of good once he realized what friendship was, long before any of the above was actually fixed, and years before it was all retconned to be a big misunderstanding, and his parents always loved him.
When Sasuke "defeated" Orochimaru the manga briefly touched on Orochimaru's past, while the anime expounded on it. His deepest dream was to live long enough to meet his parents when they were reincarnated. Years of war and loss turned him cold and bitter until only the dream of living forever remained.
Nagato lived in a state of constant war, as his homeland was the battleground for all the bigger countries' wars. For years, he was subtly manipulated by Tobi. Then, his parents were killed in front of him. Eventually, the death of his dear friend Yahiko and his subsequent crippling drove him to share his Pain with the rest of the world.
Kakuzu was imprisioned and punished for failing to kill the First Hokage. As a result he steals the elders hearts and runs away.
Kabuto grew up an orphan, but that didn't let him get down. However, he never really knew who he was meant to be. He was inspired to be a ninja by the first people to challenge him to grow in his natural talents, Orochimaru and Danzo. While on a mission for them, he was tricked by them into accidentally killing his foster mother, who in turn had failed to recognize him due to their brainwashing of her. After this happens he hits the Despair Event Horizon and Orochimaru was the only person around that was there for him at that point. He commits some good, and a lot of evil, actions for the rest of the series, but only comes into his own once Orochimaru dies and he no longer has any guidance or kindred spirit.
Obito Uchiha, after some subtle mental influencing by Madara, witnessed first-hand the death of his childhood crush at the hands of the friend who vowed to protect her and became convinced the world he lived in was hell. He then decided to accept Madara's plan to create a better world by killing or brainwashing everyone in the world.
Madara Uchiha was someone who dreamt of a peace where he could protect his last living brother in (especially after having lost many more siblings beforehand). Said brother's death at the hands of his best friend's brother was implied to have been the catalyst for his downfall—similar to the way Rin's death was for Obito's. Madara and said best friend's brother both having serious paranoia issues that played off each other in the worst way certainly didn't help.
In general, thanks to the reveal of the aforementioned Uchiha clan's 'Curse of Hatred' (which essentially mentions that Uchihas love so deeply that their brain is wired to become... unstable if they lose their most precious person, which is also the explanation for their Sharingan awakenings), every single villainous Uchiha's (well, villain) origin story can be traced back to the tragic death of a loved one.
Chapter 0, a special tie-in to the tenth movie, One Piece Film: Strong World. In it, we see Shiki and Gold Roger's rivalry, as well as the Flying Pirate's escape from Impel Down and his preparing for the movie's plot. Interspersed are scenes of people throughout the world, reacting to both Roger's death and Shiki's escape.
To a lesser extent, the Fishman Island arc explains part of what made Arlong who he is.
Charlotte Linlin is the result of her losing her mother figure and then being raised by a person who not only allowed her unsettlingdestructive tendencies but also encourage them. All of that shaped her into the unstoppable, murderous monster she is.
While he has never been a saint, as a child Kurozumi Orochi is told and convinced that there is nothing wrong with his grandfather’s treason and to hate Sakayuki and the Kozuki Clan for taking away “his” birthright, while the rest of his family got persecuted for carrying the Kurozumi name. From that moment, Orochi begins gathering money to pay a mercenary while poisoning the current shogun to inherit the throne, until he becomes a corrupted, hedonistic and evil ruler solely to take revenge on Wano's population.
Subverted in episode 10. It seems to be one of these for Homura, but instead, it ends up showing that she's far less villainous than she seems (all of her Anti-Hero antics are an attempt to prevent Madoka from dying and/or suffering a Fate Worse than Death). Played straight for Kyoko in episode 7.
Played straight, however, in Rebellion. Homura's infatuation with Madoka causes her to trick her into appearing again, so she can steal her powers of godhood and become the devil. She does this to create a new perfect world where she believes Madoka will be happy (even though Madoka didn't want any of it) and will always be by her side.
The mobile app Magia Record reveals how Nagisa Momoe turned into the witch Charlotte, who famously and memeticially bit Mami's head off. Her magical girl idol and her mother were both murdered by a serial killer, and the resulting trauma caused her to witch out. It also doubles as a reveal for the identity and backstory of Urhmann, another witch whose identity was unknown to the fans until then.
Rave Master: Almost every villain gets at least a chapter for this. Some are a little sad, some will leave you temporarily cheering for the villain (until you remember that every single one aims to wipe out all life as we know it).
RahXephon: One episode presents the back-story of Makoto Isshiki, a cold-hearted seducer and major jerk to everyone else. It shows him as a cute and kind boy who just wanted to find his parents. Then, one day he admitted to himself what he really was, and his flashback ends with him getting an Important Haircut and taking on his nasty personality.
Romeo × Juliet practically drops it line for line with the episode "Darkness: The Origin", which gives Prince Montague a somewhat run-of-the-mill Freudian Excuse.
The Rozen Maiden Ouvertüre OVA explores the start of Suigintou's fierce rivalry with Shinku and the source of her massive inferiority complex that motivated her to become the first season's Big Bad.
Tantei Gakuen Q: Confession, and... and Paths that Never Cross explain how King Hades starts his path of villainy and his rivalry-turned-archnemesis relationship with Morihiko Dan since high school. He was an honor student who was insecure about being the son of a serial murderer mother with a modus operandi of taking advantage of people's anger to make them commit the murders on her behalf, just like what he does years later in the form of an organization. Unfortunately, one of the school bullies found out about this, and bullied him for it. Too bad that one of the perks of being a serial killer's son in this manga is that he can literally burn them while he suffers no consequences even after admitting his part in it and somehow put the blame on those bulliesnote He mixed unused chemical supplies which he got because he was on a lab assistant duty that day, and "out of fear that throwing them away will endanger the teacher," he poured them into an unusable bathroom stall but he "didn't know" the bullies hung out there to smoke.
Tokyo Revengers: Despite Mikey's kindness and fierce protectiveness towards those close to him, he's shown many times to have a ruthless side and is noted to have an inner darkness that consumes him without the presence of the positive influences in his life. In multiple timelines, he ends up letting Toman become a full-fledged crime syndicate committing every crime imaginable. In the final arc, Takemichi goes back in time despite saving all their other friends to stop Mikey from falling into his darkness and becoming the leader of Bonten, Japan's worst criminal organization.
Toriko: Midora starts to reminisce over his past during his battle with Ichiryu. The flashback chapters reveal how a nameless baby born to be fed to wild pigs eventually became one of the most powerful and dreaded beings on the planet.
The flashback arc in both incarnations seems at first to be the background for the highly mysterious lead, but it's even more about the Start Of Darkness for the Big Bad, his Evil Twin. In the anime version, the kid was always somewhat touched in the head, and one abusive crewman, combined with the awareness that the human race destroyed the Earth and are now looking for a new planet, push his pragmatism into Kill All Humans territory. In the manga...he has muchbetterreason.
Legato also gets one of these, in the manga. Unusually, it has a very upbeat ending — because psychotically serving an Omnicidal Maniac who doesn't really give a damn about you is so much better than being raped to death by the guy who owns you. Knives didn't just spare him, he even asked his name! And nameless-boy-who-would-become-Legato goes stumbling after him naked and weeping for joy.
Livio has one, too, although his is complicated by the fact that first he got a psychotic alternate personality, and then later he was acquired by the Eye of Michael and turned into a killing machine in his own right.
Anime Wolfwood also gets one. Manga Wolfwood just gets back story snippets. But because the anime is Lighter and Fluffier, Wolfwood's philosophical position has a lot less pull there, so he needs a more clear-cut 'reason' to think the way he does.
YuYu Hakusho: The antagonists in seasons one and two are shown to have become villainous due to major psychological trauma leading to crises of faith in their formerly-held ideals (the massacre of Toguro's students by a youkai and Sensui's exposure to the depravity of humanity and then the Black Chapter tape). And in both cases enough self-hatred to stage really stupid, selfish Thanatos Gambits.
