King Desmond makes no bones about the fact that he loathes his son Zephiel and tries to kill him twice. Is it any wonder this wise, gentle boy grows up to be such a bastard in Fuuin no Tsurugi?
Sonia raised Nino as her daughter, but only to use her as a pawn in her evil plans. Then she ordered her assassinated, but thankfully the assassin cared too much about Nino to go through with it.
In Fire Emblem Tellius, Ashnard's treatment of his son is more a case of Parental Abandonment, but the fact that he used his son to lure a dragon to his side, and the fact that he kept the boy separated from his mother even after abandoning them both, probably falls into the "abusive" category. Soren's foster parents weren't much better: his first foster parent was verbally abusive incessantly and to the point that she was blatantly happy when he was being taken away and his second worked him for ridiculous hours and treated him (a four-year-old boy) like a full-grown apprentice. Oh, and none of them bothered to teach him to talk. He turned out to be just as good a strategist as his birth father, but he was also fiercely loyal to Ike, his Living Emotional Crutch, and also grew up to be a Stepford Snarker.
Noire reveals that her mother Tharja would abuse her by casting hexes on her and using her as a guinea pig (although this is somewhat Played for Laughs since cursing Noire to have a runny nose for three straight days seems to be among the worst Tharja does). However, Noire also mentions that Tharja did sacrifice herself for her during the events of their Bad Future, and she was not taught how to cast hexes either, but their interactions involve Tharja cursing her or acting cold towards her anyway. This mistreatment makes Tharja a divisive character to some fans.
Not technically her parents, but the Gestahlian Empire from Final Fantasy VI was the closest that Terra Branford could call her parents due to Gestahl murdering her birthmother and then kidnapping her child, and subjecting her father to various experiments. And, sure enough, their raising her was very much abusive in terms of emotional and possibly other forms of abuse. She was raised in a loveless environment for most of her life, Kefka placed the Slave Crown on Terra to manipulate all of her actions, including burning 50 of their finest soldiers alive, and the one person who was even relatively decent to her, General Leo Cristolph, nonetheless placed the mind control device back on her when they finish training.
Hojo and Lucrecia from Final Fantasy VII did genetic experiments on their son while he was still in the womb in the name of science. The child, Sephiroth, did not take this well. Lucrecia at least harbored some regret for her part in the genetic experiments, even causing her to nearly commit suicide. Hojo, on the other hand, had absolutely no regret for what he did. In fact, he enjoyed every single moment of it even afterwards, and was heavily implied to have manipulated all of Sephiroth's actions and everything in Sephiroth's life/lives.
In Final Fantasy X, Tidus's father often insulted and berated his son for being a crybaby. After believing Jecht had died at sea, Tidus's mother also pined and eventually died. As a result, Tidus harbored bitterness towards his father and never quite forgave him for it. While it's made clear Jecht actually did love his son, the man never, at any point in his life, told him such - throughout both that game and Dissidia, Jecht only admits his love for Tidus when the younger man is either absent or unconscious (or when he himself is dying).
Braska comes off as a close second if taken out of context. Before he set off on his pilgrimage he apparently hadn't arranged any kind of carer for his 7 year old daughter except after his death : Auron was supposed to take care of her but couldn't since he got killed by Yunalesca. Since Yuna is half-Al Bhed and almost everybody that isn't Al Bhed loathes them, that isn't too hard to believe that no one would look after the child of an heretic marriage ; he can't even count on her mother since she was killed by Sin, the very event that motivated Braska to begin his pilgrimage. We know this because during her video will (the sphere that Tidus stole) she explains that whilst coming to terms with the fact she was now orphaned ; she would've been left alone if Kimarhi hadn't picked her up to fulfill the dying request of Auron and taken her to Besaid. For this, Yuna remembers him very positively instead of hating him.
Cid of the Lufaine is revealed in Dissidia to be the father of Chaos, and later the Warrior of light. While he technically only acted according to the circumstances put upon him and his family by the state seeking to exploit his wisdom, he appears to be responsible for the creation of the cycle's of war between Chaos and Cosmos. Thankfully, he later becomes horrified by what his desire for revenge had done and tired to correct his mistakes.
And the cycle continued. In one of the spin-off series, Cyrus is, for all intents and purposes, father figure to an orphan girl. Who he raised as a war machine, constantly telling her that everyone is alone in the world. It's implied later that she didn't realize that kindness existed, because he didn't either. Fortunately for her, she got better, and later, so did he.
Cyrus' parents were horrid perfectionists, true, but they were consistent. In Pokemon Black And White Ghetsis goes Up to Eleven in the manner with which he raised N, teaching the boy values that directly opposed what he (Ghetsis, that is) believed in and exploiting N for his own personal gain. The revelation at the end that the boy was merely a tool to those ends is the icing on the cake, the capper to his Garchomp flight across the Moral Event Horizon. You won't find anyone in the know who isn't ready to accept Ghetsis as possibly being the prime exemplar of this trope.
Pokemon Ranger gives us Gordor, who forced his four kids into joining his criminal gang and brainwashing Pokémon. When they finally wise up and leave to embark on their music careers, he just scoffs and goes about his merry evil way. He doesn't give two craps about them and saw them as just more goons.
In The Elder Scrolls V: Skyrim, Lemkil of Rorikstead blames his twin daughters Sissel and Britte for his wife's Death by Childbirth and abuses them while complaining to everyone in town about them. In fact, if you kill him, you may get a thank-you letter from Sissel.
ZHP. It's eventually revealed that the Main Character's parents constantly insulted and belittled him ever since he let himself and his sister get kidnapped 8 years ago. However, soon after this is learned it is revealed that the kidnapping was not Main Character's fault (he actually tried to stop it, but his sister was unable to vouch for him due to Trauma-Induced Amnesia). Once this is learned, the parents quickly clean up their act. The trauma of the incident caused the mother and father to constantly argue with each other when they're not busy insulting the Main Character, while his sister lashed out all everyone else because, due to her amnesia, she has no idea why everyone in her family was mad at each other.
In Tales of Symphonia, Zelos never had the nicest relationship with his mother, as she was forced into a loveless marriage, even though she "probably loved someone else". When she's killed in an attack that was intended to kill Zelos, her last words to him were "You should never have been born". It's shown in the manga that even before this, she was cold and dismissive of her son, often making the excuse that she's ill or has a headache to get out of having to see him. No wonder he's so messedup...
In Guilty Gear X, Sol Badguy takes part in bounty hunting after Dizzy. He finds her and beats her. And it's possible not only that he is her father, but also that he already knew it, when he went after her.
Baek Doosan's backstory in Tekken 2 involves him having to put up with a decidedly unpleasant and abusive father, a result of alcoholism after a crippling injury forced him to leave Tae Kwon Do. How bad did it get? To the point where a sparring session degenerated into a fight in which Baek killed his father by accident.
Becomes a recurring theme in Grand Theft Auto IV, as the main character, Niko Bellic, and his cousin, Roman's, fathers were violent alcoholics who would regularly beat up both their children and their wifes. Dwayne Forge and Packie McReary had similar childhoods, and while the first comments how he felt "nothing" when his father was murdered, the second will at one point open up to Niko and tell that his violent father at one point even attempted and would have succeeded at molesting him, if his older brother, Gerry, had not intervened at the last minute.
In the Japanese version of Earthbound, when Porky and Picky get back home at the beginning of the game, their father chases them offscreen, and can be heard spanking them. In the American version, this is changed to the sound made when enemies in battle use "word attacks," implying that their father was only scolding them.
Then again though; this happens so early in the game people can easily assume it's not supposed to be a "word attack".
In a scene near the end of No More Heroes, it's revealed that Travis' father constantly molested his sister. She eventually gets revenge by killing him, his wife, and attempting to kill his son. Although, having a sexually abusive father is quite possibly the most normal thing about her story...
In Metal Gear Solid 2: Sons of Liberty, Emma was stated to have been sexually assaulted by her second stepfather, to which she injured him in self defense shortly before graduating from High School. The game itself doesn't specify what kind of assault it was, but the script included in the Document of Metal Gear Solid 2 had in brackets "sexual" right before "assault."
Otacon, to a certain extent, underwent this with his stepmom in the same game, although Otacon claimed she "seduced" him, implying that his part in it was willing.
In Metal Gear Solid: Peace Walker, Paz Ortega Andrade, real name Pacifica Ocean, according to her diary tapes, was an orphan, and was apparently adopted by Cipher (in other words, the Patriots faction run by Zero after the split), and she intends to obey Cipher's command, not simply due to her loyalty to the organization, but because she feels as though she has to obey them even if she doesn't agree with their goals because she'll otherwise suffer a fate worse than death if she doesn't.
There's also the fact that they created the clones of Big Boss. The fact that they were created without Big Boss's consent would make this a form of sexual abuse. Oh, and the project that created them also had six of their brothers essentially murdered during development so they could gain strong fetal growth. Then there is the fact that they kidnapped Olga's child, Sunny, after birth, and put her life on the line by having her life being connected to Raiden's vital nanomachines, meaning if he dies, they kill her, and it is heavily implied that even after Raiden defeated Solidus Snake, they still are placing her life on the line as a threat to Raiden, and she grew up completely withdrawn from people until the Patriots finally bit the dust. As a silver lining, Otacon (and to a lesser extent, Snake) do care about her and finally Otacon officially adopts her in Metal Gear Rising: Revengeance
Raiden had it rough too. The only parental figure he ever had was Solidus and he raised him as a soldier and twisted him in every possible way; on top of that, Solidus was the one who killed his birth parents. It takes a LONG time for Raiden to overcome his trauma, thanks to Rose and his son, John.
Bioshock has Sofia Lamb. An incredible list of abuse, mostly of the mental variety-though a degree of neglect etc. Attempting to condition your child in to the 'Peoples Daughter' (an individual who knows everything, or more accurately a conduit for everything), using a serum that reduced a fellow researcher to a sentient tumour, does not a good parent make.
Sofia Lamb may not even be Eleanor's mother, an audio log from her alludes that she did as little to be involved in raising her as possible, possibly even using a surrogate.
Silent Hill. Let's count: Dahlia Gillespie, Leonard Wolf, Thomas Orosco, the unnamed Mrs. Orosco, Walter's parents, Helen Grady, Adam Shepherd, and those are just off the top of my head. There's been, what, one good parent in the series?
At least Harry Mason, the protagonist of the first game, is a Papa Wolf to the max.
Additionally, one of the endings reveals Cheryl's mother Dahlia to be a spouse abuser. It's debatable whether she physically abuses her daughter as well, but the fact that she degrades and beats Harry in front of Cheryl at least stands as emotional abuse.
RELIUS CLOVER. This is the guy who experimented on his daughter, Ada, For Science!, turning her into a weaponized doll, Nirvana. However, he lost interest in the project about halfway through and happily turned to his wife instead, turning her into a much better and accomplished puppet, Ignis, after which he left his family's home and never came back. Meanwhile, his son, Carl, had been forced to finish the experiments he was conducting on Ada, leaving the poor little boy completely traumatized, having to show a lack of compassion and fend for himself as a Vigilante at such a young age. That's an abuse on mental, emotional and financial levles... and he went straight to physical (as in, attempted homicide) when Carl tried to get an explanation.
"You've been a very naughty boy... spare the rod, spoil the child."
We learn very early into Blaze Union that Gulcasa's father beat and neglected him when he was a young child; his father blamed him for his mother's disappearance. We later learn that said mother is also neglectful and emotionally abusive; the last thing she ever did to her child was Mind Rape him into believing himself to be human while sealing his demon blood without his consent. While her reasons for doing so were arguably well-intentioned, it still left Gulcasa with residual brain damage that prevents him from being able to realize that Emilia is his sister when they first meet. And if that isn't enough, she also reveals that she was aware that Gulcasa's father was abusing him, but chose not to come back and do something about it. All of this started from Fantastic Racism, which was also the reason that no one tried to do anything about the abuse. Luckily for Gulcasa, his childhood friends were willing to become parental surrogates, and lovingly helped him grow up mostly undamaged by all this.
Embric of Wulfhammer's Castle . He's the Duchess' uncle, not her father, and the gory details aren't given, but Bad King Greyghast was not above imprisoning, drugging, killing animals, spying on, and sexually abusing his favorite niece to control her.
All of the above happened to Alma Wade, in FEAR thanks to her father, Harlan Wade, and the Armacham Technology Corporation. (Save financial abuse, and that was because she was never old enough to have money in the first place.) Psychic Powers that made her susceptible to emotions, particularly negative ones and especially her fathers', coupled with physical and mental abuse due to being constantly experimented on, ultimately culminated in her being dragged away at her father's orders to be sealed in the Vault in an induced coma. Sexual abuse followed when Harlan Wade and Armacham used her unconscious body as a testing ground for psychic Super Soldiers, impregnating her twice and removing her from her prison only to give birth to the two prototypes. And worse still, she never got to hold her children. Needless to say, when Alma gets loose, hell follows her. So great is his abuse of her that her uber-powerful psychic ghost gets reduced into a scared, crying child whenever she feels The Creep, his psychic remnant, is around. After that, he goes and abuses his grandkids, For Science!. Swell guy.
Where to even start with Fei from Xenogears? After she got possessed by Miang, Fei's mother started experimenting on him, thus creating his Superpowered Evil Side Id, who then was used by his father possesed by the personality of one of Fei's former Incarnations as a Person of Mass Destruction, and that's not even all of it.
Lucien from Runescape was already notorious for being cruel, but the newest Fremminik Saga has confirmed rumors of him having a daughter. Specifically, a half human, half Mahjarrat daughter whom he abuses severely. Every time he speaks to her, he calls her a failure, finally declaring that when he next sees her, he will strangle her. And she just takes it.
Morton's grandfather felt this was the way to instill character in his grandson in The Dream Machine.
In Catherine, both Todd and Archie have issues with women that stem from abusive parents: Todd's dad was a successful businessman, but also a shameless womanizer who constantly belittled Todd, and even attacked him with an axe at one point. Archie, on the other hand, spent most of his childhood locked naked in a basement and was regularly sexually abused by his mother until the day he managed to escape and run away from home.
In The Way, the parents of two characters are revealed to be abusive late in the game. They are Traziun's dad, and Slade's mom.
Borderlands 2 has Handsome Jack, who hooked his Siren daughter Angel up to a machine that pumps her full of Eridium so that he can use her as both a living supercomputer and a catalyst to charge the Vault Key. The sad thing is that despite all of this, Jack does seem to genuinely love Angel in his demented way, but is too insane to see that he's put her in a hellish state of living from which death is the only release. Her death (which she begs for) at the hands of the Vault Hunters drives him into a massive Villainous Breakdown.
Razputin's father in Psychonauts, who puts him through tough, acrobatic circus training rather than allow him the use of his Psychic Powers, actively discouraging the use of the latter. While we don't see any of it, it apparently got so bad that Raz actually started questioning if he was simply trying to get him killed while making it look like an accident. At least, that's what Raz thinks. At the end of the game, we learn that his father is a kind and loving man who just wanted to make sure Raz didn't become over-reliant on his psychic abilities... and he's a powerful psychic himself. Raz simply misunderstood his intentions.
It's hard to say for sure, given the symbolic nature of the level he is in, but there's definitely a possibility that this is the case with Oleander's father, a.k.a The Butcher. Very little is factually known about him, other than the fact that he killed and butchered his son's favorite pet bunny right in front of his eyes, apparently in an attempt to teach him the family business.
Gloria Von Gouten's backstory heavily involves her mother, who abandoned her at a young age in order to pursue an acting career. The boarding house she left her in was not only very harsh, but it forced Gloria to pursue acting herself, which was something she was never even interested in in the first place. Once Gloria finally got out, however, she ended up becoming an even more successful actress than her mother, who soon committed suicide out of jealousy. Its implied that her mother knew full-well that doing this would be emotionally traumatic to her, and it was her death that finally made Gloria go insane.
Clem's father is implied to be emotionally abusive. One of his Campster discussions states "My dad says I'm a total idiot when it comes to canoeing. And most other things. He said he'd rather ride a seal into a pool of sharks than ride in a canoe into the lake with me. Sometimes I wonder if he's right — if I am to stupid for this world."
In Assassins Creed III (and partially alluded to in Revelations), it's revealed that Desmond's father was physically abusive to him from a young age, ostensibly as part of his Training from Hell, and that this probably played a part (though wasn't the whole reason) in why he ran away from home at 16. In the present day, Desmond hates his dad but is still desperate for his approval. William himself admits that he "did a shitty job" raising Desmond and apologizes for it.
Beyond: Two Souls depicts the protagonist Jodie Holmes' father being verbally abusive to her; he even calls her a monster to her face.
The Binding of Isaac has Isaac, the player character, actually fight the abusive mother, who deprives Isaac of his toys, his clothes, and eventually seeks to kill him.
Queen Larrsa of Mushihime-sama Futari is so protective of Aki that when Aki dies, she goes completely apeshit and wants Reco dead, to the point of sending out entire armies to kill her. Palm, Aki's younger brother, believes that Reco is not a bad person despite having killed Aki. Larsa's response to this belief is to disown Palm. When Palm comes back later, she tries to kill him, using the same amount of strength she would use on Reco.
Prototype: Alex Mercer's mother was in jail for the first nine years of his life, and when he was returned to her care at age ten, he actually preferred the various foster homes he was shipped around to over her care.
Ares, as revealed in God of War: Ascension. While not actively abusive, he conceived Orkos with Alecto with the sole intent of creating a perfect warrior to support his Evil Plan to overthrow Olympus, only to disown him when Orkos turned out to be a disappointment. Likewise, the Furies manipulated Orkos into aiding their work in punishing traitors and oathbreakers, only to imprison and presumably torture him when he turned on them to help Kratos.
In Dragon Age: Origins, this is seen in the Dwarf Commoner Warden's origin story. His/her father split years before the events of the game, and the alcoholic mother is verbally and emotionally abusive to the player character and his/her sister Rica.
Flemeth, Morrigan's mother, also fits the trope. Morrigan's dialogue with the player character suggests that she would have liked to be able to love her mother, but Flemeth's various levels of abusive behavior made it impossible. And that's before Morrigan learns that she was conceived as part of Flemeth's ongoing Grand Theft Me method of living indefinitely.
Alistair was raised by Arl Eamon, his biological father's brother-in-law, in Redcliffe Castle. Except he wasn't really raised in the castle; he mostly lived in the kennels with the dogs. He once had to stay in a cage there for an entire day after he accidentally locked himself inside of it. Then, Eamon got married, and the new lady of the house got rid of Alistair within a month - convinced he was her husband's bastard, she made Eamon pack the ten-year-old boy off to the Chantry. He claims that Eamon was good to him, but it's hard to see it that way when you know the details.
In To the Moon Johnny's mother turns to be this when it is revealed that she always favored Johnny's twin brother, Joey, over him, and when Joey was accidentally killed by his mother she made Johnny take beta blockers which caused him to forget his childhood and his dead twin brother, and then she forced Johnny into becoming a copy of Joey right down to calling him "Joey", even on his wedding day.
In Dragon Age: Inquisition, Dorian's relationship with his father was ruined when he discovered that his father rather than accept Dorian's homosexuality, planned to use Blood Magic to re-wire his brain so he'd be straight. That there was a good chance it would have left Dorian a brain-dead vegetable didn't seem to concern him. Dorian was so hurt by this that it cemented his decision to leave Tevinter to join the Inquisition. His Personal Quest involves escorting him to meet with his father, who seems genuinely sorry for betraying his son's trust and is there to beg for forgiveness. The Inquisitor can encourage Dorian to forgive him or not; either way, Dorian admits that his relationship with his father will never be fully healed.
And near the end of the game, it's revealed that Flemeth's viewpoint wasn't that she was being cruel to Morrigan, but rather hardening her for how harsh the world can be, and that she was never in any danger of a Grand Theft Me, as it needs to be done willingly.
The main characters of Lisa the First and Lisa: The Painful RPG are haunted by their incredibly abusive father. The First takes Lisa through a World of Symbolism showing how she's haunted by Marty's actions, while Brad Armstrong copes via crippling addictions. When Brad meets up with Marty near the end of The Painful RPG, he has become The Atoner, trying to make up for his mistakes by trying to be a better parent to Buddy than Brad ever was.