Many people online should at least have some awareness of the Allegedly Free GameAdventureQuest, and its prequel DragonFable. Both games are full of puns (we aren't kidding, even the designers and game characters lampshade this) and are generally very comedic in nature, but the way they create their villains are a lot more mature than they let on:
Drakkonan used to be a friendly blacksmith apprentice. His entire hometown was burned to the ground by a massive fire dragon, and the main hero of the story (that's you) failed to save his family, which caused him to befriend a less-than-stable fire mage named Xan. Xan teaches him how to cast fire, and Drakkon becomes one of the most legendary villains in the game's history.
Sepulchure used to be a legendary hero in the DragonFable timeline, but then he lost a "loved one" and apparently began to fall, and fall, and fall... until he went from being a Fallen Hero to a class-A Big Bad.
Mir from Ar tonelico: Melody of Elemia is a source virus that invokes Kill All Humans plot fairly because they were horrible jerks that abused her terribly beforehand. The heroes have to acknowledge her traumatic past before going to fight her, otherwise you get a bad ending.
Shar-Teel, a character who can join your party, is classified as Lawful Evil and she Does Not Like Men. Her biography says that she also hates Flaming Fist mercenaries and that "...likely her childhood was not of storybook quality." This all makes a bit more sense when you meet her father; he's one of the villains in the game, and he's also a corrupt member of the Flaming Fist.
Big Bad Sarevok is the protagonist's half-brother and the son of the evil god Bhaal, and he didn't have the best childhood, to say the least. His lover asks you to subdue him rather than kill him (she'll help you only if you agree) for this reason. Later, when she tries to fight you in order to protect him, you can decide not to fight her (in what would lead to her slaughter, she knows this). This shakes her out of her delusion and helps her realize that while you are both tied to the same destructive heritage, he has chosen his path, and has no real excuse. She then steps out of the way. On a similar note, the good-aligned path in Baldur's Gate II: Throne of Bhaal is to accept that Sarevok could just as easily have turned out like the protagonist and vice versa had their childhoods been swapped.
Most of the villains sport twisted backstories portrayed with varying degrees of sympathy and tragedy, but the games do make it clear that they're insane tyrants beyond redemption.
Dr. Tenenbaum defies this trope explicitly in one of her diary entries. She was a prisoner at Auschwitz, where she discovered science the Nazi way, but says that she saw them as kindred spirits, not tormentors.
Borderlands: The Pre-Sequel! gives Nisha (the Sheriff of Lynchwood in 2) and to a lesser extent Wilhelm reasons for why they became the way they are.
Nisha grew up with an abusive mother, and her only friend was a puppy who one day got bitten by a creature, went rabid, and attacked her while her mother laughed. This caused her to develop a loathing for puppies, thus why she murders Brick's dog in front of her.
Wilhelm had a severe degenerative disease as a kid which required him to get constant surgical implants, which led to a full-on addiction to cybernetics. This, coupled with the fact that the only thing he's good at is fighting, turned him into a brute who cares only about money and physical augmentation.
Clive Barker's Undying: It is pretty clear that whatever the siblings did at the Standing Stones is responsible for a lot of their behavior (especially what they did after they died).
Dr. Jaming, whose research into Aeroharmonics reached a dead end and made him desperate, forcing him to align with Griffon to get the resources he needed to continue.
Gaspard, who was called a "demon child" because of his mixed heritage. Following his father's death, he and his mother were driven out of their home by the other villagers, and when it seems like they've finally found a place to settle in, his mother falls ill from the stress and dies.
Emperor Griffin himself. After Queen Alexandra died protecting her kingdom from power-hungry humans after the Atlamillia, he began to think that everything would be better if humans were dead, so he decided to arrange just that.
Bulleta/B.B. Hood in Darkstalkers... maybe. It's implied that she really is Little Red Riding Hood, with all that entails, which would explain her explain her murderous hatred of all monsters. However, this has never actually been outright confirmed or disproven.
In Deadly Premonition, the killer is revealed to be George Woodman. It's also revealed that he had an abusive mother who beat him so bad that she left horrible scars on his back, as well as one on the side of his face that still bleeds when he becomes emotional. During the boss fight, after he's seriously injured for the first time, he starts begging for his mother not to beat him. It's also revealed that George was holding his hatred for women deep inside because he was in love with Emily, who he believed was special, but started his killing spree after she rejected him and let himself be manipulated by the game's true Big Bad.
Dead or Alive: Not a villain, but would you believe that Jann Leewas once just a scrawny Chinese kid whose upbringing was marked by bullying and poverty? He turned to Bruce Lee films to escape the misery and eventually vowed to master Jeet Kune Do and never be picked on again.Arrogant Kung-Fu Guy, to be sure, but he has every right to be that way.
All the stuffed animals in Die Anstalt are crazy, and part of the puzzle in the game is figuring out why:
Lilo the hippo is withdrawn to the point of autism because he blames himself for one of his former owners getting caught cheating on a math test.
Kroko the crocodile is paranoid and afraid of water because he was abandoned in a public restroom and used as a mop-head by the cleaning lady, who callously discarded his beloved hot-water bottle.
Dolly the sheep seems to have a canine Split Personality because she's a reversible plush (sheep on the outside, wolf on the inside) who repressed her "other self" after being used as a chew toy by a dog.
Sly the snake is prone to hallucinations because he was used to hide his owner's drug stash, and was abandoned on a highway so they wouldn't get caught. After getting his tail run over by a passing car, his body absorbed some of the hallucinogenic drugs which were stored inside him.
Dub the turtle is obsessed with exercise because he was lost at an airport, and was unable to catch up to his owner because of a moving sidewalk.
Dr. Wood is a psychologist with a few issues of his own that culminate in him succumbing to narcissistic personality disorder and starting a cult. This is because he spent years in a display case in a pediatrician's office, watching children who wanted to play with him but couldn't.
In Dragon Age II Meredith's Freudian Excuse for being an extreme Knight Templar is revealed if you are supportive of the Templars throughout the game. Her younger sister was a mage, but Meredith's family hid her so that she wouldn't have to go to the Circle. Her sister lacked the strength and training to resist the demons of the Fade, and she became an abomination that killed the rest of Meredith's family before she was put down by the Templars. As far as Meredith is concerned, any leniency towards Mages could lead to similar tragedies. She conveniently leaves out the detail that her sister didn't become an abomination until the Templars were literally on their doorstep.
Dragon Quest V: Prince Harry is a spoiled, jerkass brat because his mother passed away and was replaced by the Queen Consort, who is more interested in caring for her own son than for him. Of course, as Pankraz points out, his father, unlike his stepmother, does care about him, and would be terribly upset if anything happened to him.
In Dragon Quest VIII, Marcello, manipulative Jerkass extraordinaire, is revealed to be the child of an affair between a sleazeball noble and his maid. When the noble's wife gives birth to a son, who happens to be Angelo, the noble ousts both the maid and the young Marcello without a penny to their name, just to cover his tracks. Marcello's mother soon afterward died of sheer despair, leaving Marcello alone to struggle to survive in the world, eventually joining the clergy. However, throughout his time in the clergy, several of the higher-ups constantly looked down upon and outright insulted him just because he was of common blood, despite the fact that he quickly became a prominent figure in the church's Templar branch. All of this resulted in what Marcello is in the game proper: A bitter, condescending, overly ambitious prick who blames Angelo for everything he went through, and while this is technically true, he takes his bitterness over it way too far.
The Big Bad of Duel Savior Destiny, Downy Reed, is evil because when he was young, he and his sister (like many others where he lived) were forced to fight to the death for the amusement of some corrupt noble. When he grew up, he tracked down the noble with the intent of getting revenge, only to find out that the man had died peacefully in his sleep surrounded by friends and family. Completely devastated by such an unfair world, he swore to remake it.
Oblivion has Bellamont, an assassin who turns on the Dark Brotherhoodand tricks you into murdering most of their leaders. According to his diary, he was driven insane after watching Lucien Lachance murder his mother and joined the Brotherhood so he could murder them one by one in revenge. He still keeps his mother's head and apparently has delusions of it speaking to him.
The Dawnguard DLC reveals that this is part of the backstory of the Falmer. Knight-Paladin Gelebor, the last surviving uncorrupted Snow Elf, explains that the Falmer chose to blind themselves to avoid extinction at the hands of the ancient Nords and submitted to the Dwemer by their own volition, and that how they devolved into the Falmer of today didn't happen because of that but for other reasons.
Arch-Curate Vyrthur blames his god Auri-El for him becoming a vampire. He believes that Auri-El betrayed him by not protecting him from the affliction, and created the prophecy of the Tyranny of The Sun to bring about an eternal night to get revenge on him.
In one instance of Fallout: New Vegas, the player can take advantage of this with a high enough Medicine skill (and thus sufficient knowledge in psychology), telling an angry Supreme Chef that his tendency of yelling at people is him projecting his daddy issues. Upon realizing how shitty his childhood was, the chef will then run off and cry, leaving his kitchen to you.
Cait, the Fighting IrishDark Action Girl in Fallout 4, had extremely Abusive Parents who kept her specifically so they could sell her into slavery on her 18th birthday to a group of raiders, with the obvious implication that she was used as a sex slave. After five years, she managed to save up enough caps to buy her own freedom, then returned home and killed her parents. Even if you tell her that you think she was justified, she's still haunted by the deed and that more than the years of abuse is what drove her to become a Psycho-addicted pit fighter and implied Death Seeker.
The Nintendo DS remake of Final Fantasy IV gives this to Golbez. His father was killed by the town for teaching magic, and his mother died giving birth to his younger brother, Cecil. The hate he generated was enough for Zemus to manipulate him into stealing the crystals. According to Takashi Tokita, this was originally written down in the script, but 3/4 of the script was removed in the Super Famicom version, and it wasn't until they made the DS remake that they could implement it. In other words, the DS remake was actually more of a director's cut.
Downplayed with Final Fantasy VI's Kefka, who's insane because the process that made him a Magitek Knight shattered his sanity.
Sephiroth from Final Fantasy VII was raised by his father, the evil mad scientist Hojo, who regarded him as little more than a human lab rat and was trying to turn him in to the perfect super soldier. Obviously, Hojo mostly succeeded. Being told that his mother died giving birth to him and then finding out that his "mother" is a monster couldn't have helped, either.
Everything regarding Anti-Hero Squall's screwed-up mental state can be traced back to separation issues at a very young age when Ellone was taken away from him at the orphanage. This is compounded by an apparent complete lack of emotional support following their separation, and by the fact that junctioning Guardian Forces during his training caused him to forget his childhood, making it impossible for him to re-evaluate his childhood trauma from a more mature perspective.
Ultimecia's whole motivation behind her evil is being feared and hated for something she hasn't even done and doesn't know she's going to do yet.
One was given to the recurring villain of Final Fantasy X, Seymour Guado. In a nutshell, non-human dad marries human mum, but his species' xenophobic civilization doesn't like that their leader married a human, so she and Seymour are exiled to a long-abandoned temple. Mum decides that Seymour will need to be powerful to be accepted, so she undergoes a procedure that will allow him to call on her as a powerful summon beast but will also turn her into a statue while young Seymour is crying for her not to, effectively meaning that he's been abandoned by both parents. Summon Beast Mummy is a monster who looks like a zombie trapped in a venus flytrap with a demon for a lower half. Even worse is that after this, Seymour was expected to use said beast to destroy the monster Sin, which would make him famous throughout the land... and also kill him.
Shuyin, the Big Bad of Final Fantasy X-2, was murdered along with his lover. He became Unsent as a result, and was then imprisoned in a device that forced him to relive those murders, over and over again, for a millennium. It is entirely understandable that, on finally escaping, he devotes himself to reactivating Vegnagun, on the grounds that obliterating the country that tortured him would keep it from ever happening to him again.
In Final Fantasy XIV, there's the cruel Doman despot Yotsuyu, who was left with her aunt after her mother died when she was young. Her aunt had no love for her and insulted her by constantly referring to her as a weak child. She was given away to a drunken old man to be married, who'd beat her constantly. When he died, she was forced to work in a pleasure house to work off his debts. When the Garlean Empire came knocking in Doma, she grabbed hold of the chance to take revenge, first becoming a spy, then becoming the de facto ruler, using her power to crush the spirits of the Doman people in revenge for her treatment.
First Encounter Assault Recon's entire storyline is one giant Freudian Excuse in which the main villain, Paxton Fettel, sets out to free his mother, Alma, who was a powerful psychic who was used as a living incubator for psychic supersoldiers since she was eight years old, and had her children stolen from her in front of her eyes. Incidentally, the project lead who was behind this whole round of depravity turns out to be Alma's own father, Harlan Wade.
Brucie in Grand Theft Auto IV hates people that are poor but hates fat people even more. He only expresses his dislike once or twice and generally remains as the overbearing testosterone-filled friend to Niko. Brucie eventually opens up that when he was a child, he used to be fat and everyone at school made fun of him. Since then, Brucie has become obsessed with exercise and appearance to keep himself fit and shedding the pain he went through when he was overweight. The Ballad of Gay Tony reveals that on top of the above, Brucie's older brother Mori is (or at least claims to be) better than "Baby Brucie" in every way (we see Mori beat him at chess, force him to do pushups, and belittle him at every chance he gets, among other things), which further fuels Brucie's inferiority complex.
Trevor in Grand Theft Auto V intentionally invokes this trope, and not sarcastically either. It comes off as even less convincing here, since compared to Trevor, CJ is practically a saint.
If Ethan manages to find and save his son, Shaun, in Heavy Rain, Scott Shelby confronts him to congratulate him for passing his trials. Ethan questions him on why they gone to such great lengths just to find a capable father. The killer goes on a rant, saying that Ethan has no idea on how it was like to be treated as worthless by his own father and that he suffered just as much as his victims had. Ethan doesn't buy it.
Zane Lofton of Hypnospace Outlaw is a major jackass who nobody likes, to the point where The Dumpster breaks its "don't go after anyone under 18" rule regarding him. That being said, his comics and Tim's choice of insults against him suggest Zane comes from a poor family and doesn't know his own father, which his FLST journal confirms.
In the 1st Degree has artist James Tobin charged with first-degree murder and grand theft. The interrogation tape of Yvonne Barnes suggests that Tobin ended up doing these things because his wife Helen divorced him. However, she did that because she apparently got fed up with his ways. This would indicate that Tobin may or may not have much of an excuse for what he did.
For all the evil that he does afterwards, Ganondorf from The Legend of Zelda series has a fairly understandable reason for his desire to conquer Hyrule and claim the Triforce: His people were trapped in a lifeless desert, forced to steal from others just to eke out a life. Seeing his people in such despair and then seeing a land within spitting distance that was rich, prosperous, and inhabited by people who didn't even realize their good fortune understandably made Ganondorf very angry. Supplemental material like the official Nintendo Comics, and brief mentions in The Legend of Zelda: Ocarina of Time, hint that Ganondorf actually tried to invade Hyrule the old-fashioned way. When that failed and he was forced to swear fealty to the Hyrulian king, he turned to searching for the Triforce as a second option.
It gets even worse in Skyward Sword, where it's heavily implied that the reason behind Ganondorf's evil is because he's the reincarnation of Demise's hate, meaning he's been screwed up since before he was born to do evil. Not only that, but it's also revealed that the desert the Gerudo would eventually come to inhabit wasn't always like that. It was once as lush and fertile as Hyrule is in other games, not to mention even more technologically advanced, but was sadly stripped of its resources and left to wither away and die by an ancient civilization.
Jack was raised as a test subject and was encouraged to be violent and wasn't allowed normal relationships. She seems surprisingly well-adjusted, considering.
Miranda begins Mass Effect 2 as an Ice Queen extraordinaire. It's shown that before meeting Shepard, only three people to her knowledge never betrayed her trust. Her father is an absolutely despicable human being who grew her and her older sisters in test tubes, only to kill all her older sisters for not being worthy of preserving his legacy, viewing her as nothing more than his "perfect" property to satisfy his galaxy-wide ego. Her rescue of her baby sister and escape from her father had her join a xenophobic terrorist group, Cerberus, for protection. Her "perfection" has ironically resulted in a major inferiority complex that makes her incapable of crediting herself with her own successes. With Shepard's help she can get over this, and ends up being one of the warmest and kindest people in the series.
Defied by Kaidan. Of all the series' human squadmates, he has the most justifiable reason to have issues with Fantastic Racism against aliens in general and turians in particular. If the player chooses to suggest that this is the case, Kaidan is not amused and pointedly refuses to use his past like that on the grounds that it would be very hypocritical for a human to do so.
Lampshaded in one conversation, where Shepard randomly asks EDI if she has daddy issues about her creator The Illusive Man. When she denies it and asks why Shepard asked that, the reply is that s/he has learned from experience that something like that always pops up sooner or later in everyone they meet and it's just easier to ask.
Speedy Dave who was trying to protect the natural world. It's more left to the viewer's imagination, but it's easy to assume that the rapid modernization of the world caused him to lose his home or a childhood site he loved to visit.
Princess Pride of Creamland. Creamland was one of the first nations to go online, but was soon ignored by other bigger nations that went online later.
Gauss Magnus was born to a poor family. His brother was adopted by a rich family, but not him. Then his parents became ill and died, leaving Gauss with nobody. So he worked hard to get rich and break the society from within.
The leader, Sean, was orphaned in a plane crash. Despite inheriting a fortune from them, he was forced to live with cruel relatives and was ostracized by society. He also mentions that he was picked on, too. The internet was the only way he was able to make friends, so he played at being an adult and made net-friends in everyone else, who came together to form Gospel.
Solo was picked on, excluded, and attacked for being different as a child, and this, combined with his status as the Last of His Kind, has left him with a towering hatred of even the idea of friendship, believing that only weak people form groups.
In 3, Jack and Tia were orphaned because their home country was devastated in a war for its technology, so they worked for King to gain access to Meteor-G and destroy all technology.
It's a fairly common theme in the Metal Gear series:
A nice example is from the non-canon Ghost Babel, wherein serial-killer-turned-special-agent Marionette Owl reveals that the beginning of his gruesome murder spree stemmed from finding the love of his life disemboweled and dismembered, and realizing the beauty of death.
Dr. Koppelthorne in Metal Gear Acid 2 primarily did the stuff he did because he wanted to revive his wife who was killed.
Kojima seemed to be so set on giving Psycho Mantis one of these in Metal Gear Solid that he ended up giving him two. In codec discussions early in the game, Mantis is said to have worked for the FBI as a psychic profiler until he dove too deep into the mind of a mass-murderer and took on his personality. When he's defeated in battle, Mantis says that his murderous ways are caused by accidentally having killed his father as a child and being forced to witness that all human beings only exist to procreate, with no mention of the FBI.
Big Boss himself had to endure several of his allies being exploited by the government, sometimes just being sold out to their enemy to cover up their secrets, he was used to kill his mentor just because they didn't want to abort a mission to steal the legacy from the enemy and yet avoid nuclear war (and that's just going by the abridged version of the true reason for his being recruited to kill The Boss. In the unabridged version, it was deliberately set up that way specifically because they feared her charisma and planned her death from the beginning, and manipulated a sadistic GRU colonel into firing on his own countrymen and creating an international controversy just to have the excuse to have her killed), and his own friends use him for things, even taking his DNA and cloning him without his consent. Finally, he hits his breaking point when his entire home gets destroyed and he falls into a nine-year coma, only to wake up to find that the whole world wants him dead. Being reduced to a bitter old man with a vendetta, it's no wonder why he would end up founding Diamond Dogs, Outer Heaven, and Zanzibar Land, each a gradually decaying and increasingly warmongering and authoritarian version of his utopic Mother Base for Militaires Sans Frontieres, which was essentially an anarchist commune and one of the few times he was genuinely happy.
The title character has a pretty tragic story. Her whole backstory is revealed whether the player chooses to kill Tohma or Mr. Sohta. Years prior to the story, she was bullied by other kids. Her childhood friend, Kudoh, initially started defending her and even hung out with her. However, he started getting teased and eventually stopped spending time with her. Then, within the last few weeks of her life, she started dating Tohma, which seemed nice at first. She then found one of her texts on the school board and was targeted by Yoshino and her group. She even saw Tohma with Saotome one day and found out who posted her message. Eventually, Yoshino had a boy sexually assault her in the bathroom, and this finally broke her. Later that night, Sohta found her crying in a stall and Misao told him everything. He seemed to be understanding at first, but he then started making advances. Frightened, she let out a Big "NO!", which angered him and he strangled her. It's pretty understandable why Misao would be upset by the people in her life. Most, if not all, of them caused pain in her life and she wants some retribution for their actions.
Oddly enough, Mr. Sohta has one himself. For as long as he could remember, no one accepted him for some reason. A majority of his class rejected him for his appearance and deemed him disgusting. Even when he tried to do something nice, something would go horribly wrong (such as when he tried to save a dying cat or return a handkerchief to a classmate). One day, a girl he had a crush on decided to start hanging out with him. She seemed to be the first person to accept him, but when he confessed to her, she rejected him, claiming that her time with him was done out of pity. Because of this, she thought it best to stop meeting with him. This was the last straw for him and he finally broke. He shook her violently while demanding to know why no one accepted him. You can only access this backstory by obtaining the official ending.
The shouty guy from Mondo Medicals apparently (as far as his insane Engrish ramblings can be believed) witnessed his father dying from cancer, and this shock was at least partially responsible for his decision to begin curing cancers via killing the patients, including killing the player character under the pretense of curing cancer.
Monkey Island: Depending on your interpretation (and which games you consider to be canon), one possible explanation for LeChuck's evil aggression is his unrequited love for Elaine. However, later games indicate that he was evil before meeting Elaine (he is a pirate, after all). Tales of Monkey Island suggests that the manipulative nature of the Voodoo Lady seems to be a possible source of his evil.
Mystery Case Files: Escape from Ravenhearst is one long excuse for Charles Dalimar, who implies that his miserable childhood and commitment to an insane asylum are what made him what he was.
Invoked Trope in the background materials for the Oddworld series. The slig species are a eusocial species, and their queen beats them as children so they grow up to be cruel and sadistic. This is probably to make them attractive for when they're employed as low-cost security for Glukkon businesses.
Zashiki-warashi from Onmyōji has huge mummy issues. All the families that welcomed her into their homes were only after the good fortune that she brings, so when she meets this widow who actually treats her like her child, Zashiki-warashi goes out of her way to take the lives of young yōkai and feed them to the woman in order to lengthen her life.
Wolf's background in PAYDAY: The Heist explains that he is out stealing cash and other valuables because the bad economy made his business sink and his family became homeless.
This is an important plot point in Persona 5. The treasure within each palace is a metaphorical representation of whatever is causing the owner to act the way they do. By stealing these treasures, the Thieves remove its influence, causing HeelFace Brainwashing in the process.
The mob boss Kaneshiro is afraid of going back to being a poor and helpless nobody.
The fourth target is suffering from survivor's guilt and believes that she was the cause of her mother's death.
Rich CEO Okumura was denied a model rocket as a kid due to his family's poor funds.
The sixth target's is not revealed, but suggested to be the combined weight of her father's death, the burden of taking care of her younger sister, and trying to get ahead in a male-dominated career.
Akechi is Shido's bastard son and wants revenge on him for rejecting him and his mother.
Silver from Pokémon Gold and Silver and their remakes has one. He pushes the player character (or anybody for that matter) around, mistreats his Pokemon, and most all, detests Team Rocket with a burning passion. A deep-seated psychological excuse is hinted at in the original games, but what it is never comes to light. However, the Celebi event in HeartGold and SoulSilver reveals that his father is Giovanni, the leader of Team Rocket, who abandoned him after the events of Pokémon Red and Blue after being defeated by the hand of Red. Not wanting to be weak like his father, Silver became obsessed with strength and grew a major Inferiority Superiority Complex as a result.
Cyrus is said to have been under intense pressure as a child to live up to the demands his parents put on him. Despite being so intelligent and such a good student that people in his hometown still talk about him as such when he's in his late 20s, he could never live up to his parents' standards. His plans involve him becoming a god — a perfect being, ruling a perfect world, with perfect people, no matter what that entails.
In Pokémon Black and White, N is perceived as a Well-Intentioned Extremist since he wants to separate humans and Pokémon because he thinks that humans treat the latter like tools. The reason for this is because Ghetsis deliberately neglected him so that he would become what he is now. N was raised with abused Pokémon for a good portion of his life and believed that humans were evil (aside from his "subjects" in Team Plasma), setting Ghetsis's plan into motion so that he could make Pokémon illegal for everyone but himself so he could rule Unova. Ghetsis even tells N that he's "a monster incapable of understanding humans."
Pokémon Black 2 and White 2 shows Team Plasma (although it's only Ghetsis) as being Hugh's Berserk Button. He seems to be laser-focused on making Team Plasma pay. You learn that Team Plasma stole his sister's Pokémon. Who is now following the Shadow Triad.
Guzma from Pokémon Sun and Moon wanted to be a trial captain as a child but failed and ran away from home because of his abusive father. As a result he became bitter over the island challenge and wanted to fight back against Alolan tradition as well as assert his own strength as a Trainer. Team Skull as a whole is made up of people with similar motivations, as they're all outcasts who failed their island challenges and have to steal to support themselves.
Sasha's obsession with keeping one's mind under control stems from the incident that prompted him to leave home: an amateurish psychic foray into his father's mind to learn more about his dead mother that ended up dredging up some... rather inappropriate memories of her.
The final boss is Raz's and Oleander's Freudian Excuses combined, essentially a grotesque combination of their fathers. Subverted in that Raz's actual father helps him fight the nightmare. Turns out Raz just needed to communicate with his father more; it was really all one big misunderstanding.
Quantum Protocol: Aurora's mother, Maya, wants the former to put aside her conscience to focus on making her career successful. This is because Maya endured sexism in her own career and believes Aurora will need to more career-focused in order to overcome it.
RealityMinds: Despite all the evils she committed and her cruel personality, Kvena turned out that way because she was ostracized by her peers and her lover for her essence research, got turned into a ghost by Ridgefern, lost her only friend Refita, and went insane when it looked like Silvana couldn't send her to the afterlife.
Red Dead Redemption gives us Jack Marston, the son of the protagonist John. As his father was an outlaw and later a bounty hunter, Jack didn't really see him, and was mostly raised by his mother and a man called "Uncle" (not related to the family, a friend of John). When he was 16, his father returned once more, promising to stay with them from now on. Several following missions show John doing various stuff around the family farm, such as teaching Jack how to hunt. In the final story mission of the game, the farm is attacked by the same federal agents that John helped to earn his freedom. A firefight starts, and Uncle is killed. Later, John sends Jack and his wife Abigail away from the farm, and realizes that his family's safety is only guaranteed if the soldiers get what they want. John exits the barn, shoots at a few soldiers, and is easily dispatched by the massive firepower of the soldiers. Jack and Abigail return to the farm, and find John's bullet hole-ridden body lying in a large puddle of blood. Now the game jumps a few years into the future, with the 19-year-old Jack standing beside his mother's grave. From this point onwards, Jack is the playable character, and can be made either a man of honor or a ruthless desperado. Regardless of the player's actions, he still has a deep hatred towards lawmen.
River City Ransom has this for the Big Bad, Slick. Slick was actually Simon, a friend to Alex. He grew jealous that Alex was always better than him in everything and got all the attention, so he started the events of the game just to get revenge on Alex.
Sam: Why do you persecute harmless bigfoots? Conroy: Harmless? Harmless? I'll have you know my parents were killed by a rabid bigfoot! Sam: Really? Conroy: Well... no. Actually, I'm just a warped evil person who gets his jollies torturing innocent woodland creatures. Sam: Well, that's a valid motivation too.
In Silent Hill 2, Eddie used his humiliating childhood traumas to excuse his violent methods of coping with the way people look at him. "Violent" as in murder.
In Silent Hill 3, Vincent blames Claudia's religious zeal on her father abusing her. This apparently deeply affected Vincent as well, which raises a host of questions about just how early in life he was involved with the Order. Unlike the example from Silent Hill 4 below, however, the player is less likely to be sympathetic towards Claudia, considering what she did to kick the plot off. And then there's the possibility of how she treated the children in the "care" of the Order... even though by the end of the game, she apologetically admits to failing in her mission to turn the world into "Paradise", too. It's not enough by then. An interesting side note, however, is that Claudia herself explicitly believes that she will go to hell for her actions. So, she is working towards a paradise only for others, to the exclusion of paradise for herself.
Shadow the Hedgehog has one as his main motivation in Sonic Adventure 2. Due to the death (metaphorically) of Maria Robotnik, he vowed vengeance against all of humanity. He remembers later that Maria did not want that, and wanted him to forgive humanity since there are some good people in the world.
In Shadow the Hedgehog, we have the GUN Commander's motivation for his seemingly blind vendetta against Shadow. It turns out that he's one of the (very few) survivors of the Ark Disaster and, like Shadow, was a close friend of Maria. The Commander's hatred for Shadow is because he blames him for Maria's death, believing that if Shadow had never been "born", Ark wouldn't have been wiped out and Maria wouldn't have died. He realizes the folly of this reasoning in the True Ending, however.
Napoleon LeRoach, the Big Bad of the second SPY Fox game, was made fun of for being too short for a certain ride at the World's Fair. This led him to come up with the Giant Evil Robot Dog plot, where the giant robot is not only taller than everyone else, but also a ride that activates as soon as one million people go through the Fair entrance.
In Star Control II, the Ur-Quan reveal that their entire race has a Freudian Excuse: They were psychically enslaved until they discovered that their masters could not command beings that were in excruciating pain. After earning their freedom, they vowed to protect themselves from ever suffering such a fate again. This, in combination that the fact that the green Ur-Quan, who enslave other races, are relatively benevolent when their orders are obeyed, makes them more of an Anti-Villain. The Big Bad black Ur-Quan, on the other hand, just want to kill everyone. Word of God has it that the Ur-Quan were in fact based upon real-life acquaintances of the creators who were abused as children and the effects it had on them.
Prince Luca Blight from Suikoden II is one of the nastiest, evilest, and most badass villains ever conceived. He kills a unit of his own country's soldiers (the "Youth Brigade", even — kinda like heavily armed boyscouts), kills his father, usurps the throne, starts a war, and unleashes some Sealed Evil in a Can to depopulate a large city completely. However, when he was 6, he watched his mother being raped by soldiers from the country he's invading in the present, while his father ran to hide in the capital. The kidnap-rape wasn't just a random act of malice by enemy soldiers, it was ordered done by the then mayor of Muse. Even though the Highlands and Jowston were indeed at war, they weren't invading anything, they were non-combatants. Luca's mother died nine months later, which was when his little sister was born. The little sister grew up to strongly resemble her mother and thus serve as a living reminder of the horror that Luca had witnessed all those years ago. He's seeking revenge on both his father and the country he blames for the events.
Suikoden IV has Graham Cray, who masterminds a war and creates a Weapon of Mass Destruction... motivated by his Start of Darkness: The True Rune of Punishment, which was sealed away on Obel Island, once chose him at its host. To avoid being consumed by the rune, he chopped his own hand off... at which point it jumped to his son. Though he begged his son not to use its powers, the boy naturally ended up disobeying him, using its power to destroy the soldiers raiding their village. Oh, and the soldiers were part of a False Flag Operation being pulled by the Scarlet Moon Empire, Cray's superiors. Naturally, they blamed him for the incident, sending him off in shame to start plotting revenge. So the whole thing's just so he can try and reclaim the rune, reuniting him with some small piece of his son.
In Suikoden V, Gizel Godwin and Euram Barows share a Freudian Excuse, in a way: Both of them had loved ones killed by Nether Gate, the Queendom's cabal of assassins, during the bloody Succession War. For Gizel, it was his mother; for Euram, his elder brother, who was supposed to be his father's heir, thrusting him into a role he hadn't expected. They cope with this trauma in different ways, neither of them really all that good.
Count Bleck, the Big Bad of Super Paper Mario, had a pretty understandable and sympathetic reason for causing the events of the game: He was originally a man named Lord Blumiere, and he fell in love with a woman named Lady Timpani. However, his father didn't agree to the relationship, and thus exiled her to several dimensions, causing him to kill his father in grief and summon the void in an attempt to commit suicide. In other words, love made him evil, and it also acted as the very thing that turned him back to good so he could undo the Void once he found out that Timpani AKA Tippi was alive.
The Tales Series love making the villains sympathetic. For example, in Tales of Graces, the main villain Lambda is an all-powerful being who was a result of a team of researchers trying to save their planet from wasting away. Lambda was originally a semi-human child, and one of the researchers treated him as his son, being nice to him and teaching him things one would teach a human child. The other researchers felt that Lambda was unsafe and wanted to destroy him, killing Lambda's only friend in their attempt.
The Tiamat Sacrament: The original ruler of Ildria, King Khytiel, lost his wife, and the trauma caused him to focus the country's resources on protecting his daughter rather than all the citizens as a whole. This left the rest of the country vulnerable to bandit attacks from the Borderlands, creating enough discontent for Ry'jin to organize a coup.
Valkyria Chronicles has Maximilian, who tries to conquer the world because his mum was unpopular amongst the nobility, and then was killed.
Rasmus from Xenogears was created as the epitome of humankind and as an Artifician -Contact- until he literally got trashed as a fetus when Krelian discovered that the new -Contact- had already been born. It doesn't help that Fei beats him every single time and that his superiors consider him "trash". It turns out that Miang orchestrated this from day one, so as to manipulate him into killing Cain when the time was right.