Advice and Trust: During their talks Shinji tells Asuka how he was abandoned by his father only to be called ten years later because his father needed him to pilot a giant robot; and Asuka explains Shinji how her father cheated on her mother, and after her demise he married to his lover and refused to take care of his own four-year-old daughter. Although the worst would be Asuka's step-mother, who put her on Benzodiazepine (which is incredibly dangerous when used improperly) to make her "a placid little doll".
In A Triangle in the Stars, it was hinted at in several chapters and finally revealed in Chapter Thirty that Bill Cipher had these parents, by virtue that he was a triangle instead of a square, a pentagon or a circle.
And that's not all. Alex himself confirmed he had a much WORSE childhood than Stanley Pines did. OUCH.
Awkward Silence: Riko Shibata's mother is referred most commonly as "Ursula" for a reason. Over the course of the story, she emotionally and physically abuses Riko. We later find out that, when Riko was raped by her uncle when she was younger, her mother did nothing because she was having an affair with said uncle.
The Child of Love: Shinji’s mother chose to get absorbed into Unit 01 and for whatever reason wanted her son watching as she dissolved. Right after his father abandoned him. Meanwhile Asuka’s mother got crazy, stopped recognizing her daughter and eventually killed herself together with a doll she thought was Asuka. As she was institutionalised, Asuka’s father cheated on his wife with her nurse where Asuka could hear them, and after his wife’s death he got married with his lover and stopped looking after Asuka. Shinji and Asuka are screwed up due to this. And that was before Gendo used his son’s crush like a disposable pawn with no regard for his son’s feelings.
Digimon: Children of Time: As revealed in Present chapter 26, Rumiko's yakuza father tried to sell her as a prostitute, but Seiko refused to let him and ran away to Shinjuku with Rumiko and her then-boyfriend, Rika's father, in tow.
Doing It Right This Time: Besides the usual culprits (Gendo abandoned Shinji and ordered Rei to live in a dump and be heavily sedated, Yui actually wanted Shinji watching as her body dissolved, Asuka’s father threw her aside after getting married to his lover...) Naoko Akagi is worse than she was in canon due to Rei’s changed background. She constantly abused her little daughter emotionally and later strangled her to death.
HERZ: Shinji and Asuka suffered due to their abusive parents ditching them right after their mothers' deaths. That is the reason that they got messed-up during the Angel War, took six long years before becoming a couple and are still traumatized in their late twenties. At least Gendo is genuinely remorseful and trying to atone for his actions, but Asuka's father is completely absent from his daughter's life.
Last Child of Krypton: Shinji’s father abandoned him shortly after his mother’s death. After ten years Gendo summoned him and Shinji thought his father wanted to see him… but when Shinji failed synch with an Evangelion, he sent him back without even saying one word to Shinji. And then you have the “I’ll hurt your little girlfriend or use kryptonite with you if you get in the way” part...
In The Wheel And The Butterfly Saga, Dan's parents are confirmed to have been very abusive towards him, keeping him in a cage for the first few years of his life, in addition to the emotional abuse.
The Three Kings: Hunt: James Andrews is mentally and physically abusive towards his wife and both his children. The fic does a good job of portraying the issues that arise from abusive homes from Ryou's mental instability (kleptomania & insomnia etc.) to Amane's anger management issues
Once More with Feeling: Gendo treats Shinji and Rei like crap and doesn’t care about them at all (unlike his canon self who wanted to be a good father but didn’t know how to be one)
Shinji: You know, on some level I should be surprised that you would threaten to have a fourteen year old Girl sent to her death if I didn't do exactly what you said… but I'm not. Fuyutsuki: Now Shinji, that's not what he- Shinji: Oh of course it is. You don't have any need to defend this man in front of me. Yesterday he paraded Rei out as the consequence of me defying him, putting her through hell just to blackmail me into Unit One. Every one of us knows she wouldn't have lasted five seconds in combat, but he didn't give a damn.
In I Will Remember You, Ulrich Stern's father is a vicious, depraved man who beats his wife and son for years. Mr. Stern ultimately destroys Ulrich mentally and leaves him covered in scars and living under a new name after the latter throws his father through a wall.
Pete is clearly a psychologically Abusive Parent in the Goof Troop canon, but in the fanfic Anything Or Nothing, the author extends it to physical abuse. The lack of Social Services is explained by PJ (and his mother Peg) being too afraid of Pete to alert anybody to the problems. Consensus among reviewers is that it's frighteningly realistic in the portrayal of the abuse and how it is covered up by the family from friends and authority figures.
Shows up a lot in Brainbent. More prominent examples include Rose's mom (emotional/psychological) and Dave's older brother (extremely neglectful; emotionally and possibly sexually abusive)).
Lorelei's parents from The Lorelei Chronicles fight constantly and are one of the reasons Lorelei universe-hops so much.
Emily Hawthorne's mother from Pokemon Johto Quest is one of these as she treated her daughter like her punching bag for a while. However, she feels bad about doing this and wants to repair her relationship with her daughter.
Tabitha's parents from Total Drama Letterz not only encourage their daughter to eliminate other campers on Total Drama, but they'll also beat her to near death for the slightest failure.
There's quite a few Harry Potter fics out there that take the Dursleys' abusiveness and ramp it up to eleven. One particularly painful example is Whelp, which begins with Vernon punishing a seven year old Harry with no food [after he had previously spent two nights without food] for not cleaning the patio, even though he did clean it before Dudley tracked mud all over it. Then, when Harry tries sneaking out of his cupboard while everyone's asleep and eating from the garbage, Vernon catches him in the act and punches him in the face numerous times before locking him outside. Petunia wakes him up by spraying him with the hose, and when Vernon comes home he chains Harry up like a dog in the backyard, and gives him nothing but water and dog food for dinner. Needless to say, it is IMMENSELY satisfying when Snape comes into the picture...
One example is in The Nuptialverse, where they are emotionally abusive, constantly treating her like a foal and putting her down. When she stands up to her father, he starts beating her.
In the same series, Pinkie Pie's father became emotionally distant after his mother died, culminating in hitting Pinkie and accusing her of wasting his time when she got a cutie mark he didn't approve of (her mother didn't partake, but didn't stop him). This led to Pinkie running away and ending up in Ponyville. Unlike most examples, however, they're revealed to have eventually regretted what they'd done and try to make amends.
Helping Hoof's father forced him to act exactly the way he thought he should act, never letting him do what he wanted. As a result, he never got his cutie mark. Because of this, he called him worthless and belittled him, driving him to work for Checker.
The Triptych Continuum has multiple examples, usually related to a parent being disappointed in a child's cutie mark. Pinkie's father was extremely abusive to her, as she displayed an apparent lack of earth pony magic even before her mark manifested.
GeneralEsteem to Rarity. He's a total nutcase as he subjected Rarity to extremely harsh Training from Hell from foalhood in a attempt to make her strong and "superior" like him, killing his wife because she objected to his belief. The reason Rarity and Sweetie Belle got away from him is because Celestia's intervention.
It seems that when Drago was sealed away by Lo Pei, Shendu intentionally left him that way in order to "build character".
Jade's parents almost veer into this from Parental Neglect; Tarakudo uncovers in a dream that after injuring herself exploring (sliding down a banister), her mother's reaction was to spank her for disturbing the adults' party rather than concern for Jade's well being (she ran into a statue at the end of the railing and had severe bruising and was crying). Jade truly considers going to live with Jackie to be the best thing that ever happened to her before she went evil.
The notorious Shinra High SOLDIER has three prominent examples: Julia's mother and father forced her into prostitution when she was younger and locked her up in a mental institution for three years. Her father beat and raped her, and ultimately tried to kill her. Hojo has been physically and mentally abusing Sephiroth since he was born.
Javier's parents aren't much better - they kicked him out of home when he was in his teens, forcing him to have to deal drugs and even prostitute himself while living on the streets to get by.
Mei Shirakawa's parents in the Horseshoes and Hand Grenades sidestory Wheel of Fortune don't care about the problems their daughter has to go through regarding Yamada Tatsumori's tyranny over her High School, with the mom going as far as to leave Mei in the hospital despite going there to check on one of her friends. It's later revealed that she was supposed to be the next heir to a family fortune by showcasing her untapped psychic powers which are attuned to her stress levels. The parents emotionally abuse her to get the powers to spike. They get killed off by Renenutet.
A Minor Miscalculation takes Ragyo's canon physical, emotional, and sexual abuse of her daughters and highlights it; the fact that everyone's plans are going awry causes her to drop the excuses used in the series and openly torture Satsuki for fun and pleasure. She also violently attacks Nui - who otherwise enjoysthe abuse - after hearing of her failure to kill Ryuko's father.
My Mirror, Sword and Shield Suzaku’s unnamed mother was verbally abusive towards him, calling him a mistake and was neglectful of him, spending all their money on her drug habit. Suzaku remember that he had to take of her and himself more than it was the other way around until she overdosed when he was nine. When he accidentally time travels to the past, he deliberately decides to not help her, knowing that she won't change.
Mary Jane Watson grew up in a broken home, as she and her mother suffered appalling physical and emotional abuse at the hands of her father. This left Mary Jane with some major anger issues, and she originally becomes a superheroine for no better reason than to spite her superhero-hating father. A major part of her Character Development involves Mary Jane coming to terms with her childhood and fighting crime for the right reasons.
Little Bruce Banner was molested by his psychotic mother Rebecca Banner, who also viciously intimidated Bruce's father Brian to keep him from protecting their son. The anger Bruce felt at what was done to him, and his hatred of his father's pathetic weakness, were both major factors in his being so unstable when he became the Hulk.
Spider-Woman's enemy Polestar was repeatedly humiliated and ridiculed by his parents for not being as athletic as his older brother or as academically gifted as his younger sister. When he gained superhuman powers, one of the reasons he became a supervillain was specifically to humiliate his family by being associated with him.
The Green Goblin became an obsessive control freak who enjoyed terrorizing the people around him after he saw the way his father had destroyed the family fortune through his drunken binges and lack of self-control.
It's heavily implied that the reason that the Brothers Grimm became such Psychopathic Manchildren was because of all the cocaine their mother did while she was pregnant with them.
In The Fairly OddParents! fanfiction, Never Had A Friend Like Me, Amanda's parents are never going to win a parenting award. They never wanted kids and don't want to waste time, energy, or money on the one they ended up with. They aren't physically abusive towards her. Emotionally and mentally, however... Well, when even Norm feels bad for you, you know that the kid deserves a break.
While Vesser's parents in Hanna Is Not a Boy's Name fall squarely into this trope, his dad reaches new lows in Lightwaves. In Vesser's backstory chapter, it's revealed that he got his selkie wife to marry him by forcing her to do so in exchange for protection. When she begs to be allowed to return to the sea, when Vesser's sixteen, he responds by hitting her and then hits Vesser for the horrible crime of staring in horror at the action. When Vesser, reacting purely in fear, bites his dad, Mr. Hatch reacts by calling the police to have his wife and son be arrested as Undesirables, leading to Mrs. Hatch's death and Vesser becoming an outlaw. The entire thing basically turns Vesser against all humans in the city.
In Dead Of The Night, Conrad's dad berated his son for "terrible" life choices like wanting to be an artist, generally belittling him at every chance he got, before leaving the family. Conrad's mom, meanwhile, subjected her son to her many, many anxieties, leaving him something of a nervous wreck. On Vesser's side of things, his mother was implied to be crazy (even by selkie standards) and couldn't decide if she wanted him around or not, so she enchanted Lee into watching Vesser while she was in the ocean for years on end.
In Yet Again, Hinata and Gaara deal with theirs in different ways. Hinata grows a backbone, promptly snaps from all the stress and repressed sexual tension, and shows her entire clan what she's capable of, effectively scaring them into submission. Gaara simply allows Orochimaru to kill his father... again.
John Gage in this series of Emergency! had abusive uncles as surrogate parents in his backstory. So very,very much. They had him after his parents died and it was not pretty. His aunt rescued him eventually.
In the Card Captor SakuraContinuation FicShadow of the Dragon, school bully Satome's mother Himiko, Tomoeda's district attorney, is revealed to be one, constantly beating him because he is the product of rape and she only sees him as a reminder of said rape; as a result, Satome has become a Straw Misogynist and serial rapist. In chapter 19, when Satome is in jail for his Attempted Rape of Tomoyo, he tells the lawyer assigned to him that his mother put him in the hospital eight times for a total of fifteen broken bones, and that he's perfectly willing to confess to all of his rape charges as long as it keeps him away from his mother until he's twenty. Shortly after, however, his mother arranges for him to be assassinated and his death ruled as a suicide because his status as a rapist would reflect poorly on her career of prosecuting sexual predators.
The Elfen Lied fic Family Sticks Together has this in the backstory of Alex. Prior to ending up in the orphanage, Alex lived with his maternal uncle, who beat him regularly, called him a freak, and locked him out of the house to fend for himself. When conversing with the spirit of his mother in chapter 10, she explains that she left the infant Alex in his uncle's care to protect him from Director Kakuzawa and his mooks, though she admits that, given his uncle's treatment of her son, it probably wasn't the best choice.
In the Pretty Cure fan fic, Twilight Pretty Cure, the Big Bad of the series, Zenjin, was abused by whom the fairies call an evil woman before the Rozanielans rescued him. Nobody knows who the woman is. It's implied that this caused his sociopathic, psychopathic, and homicidal tendencies.
In Gensokyo 20XXI, while not her mother, at least technically, Kanako clearly fits in that she would beat Sanae to vent frustrations and over minor infractions. It was noted throughout the rest of the series that, while she regretted abusing her, she didn't get a chance at redemption, as Sanae had died (before being brought back from the dead through Yukari's reality warping).
Ghetsis displays this type of behavior in Natural Liberated, although N is not technically his biological son. He exposes N to abused Pokemon in order to make him believe that he must free them from trainers. Such abuse is the Freudian Excuse that N uses to justify his freeing of Pokemon from people, the first and the second time.
Son Of Apophis, a Yu-Gi-Oh! fanfic, takes the abuse Marik experiences to a whole new level. His father actually attempts to mute him.
Nobody Dies, a Neon Genesis Evangelion fanfic, features Kyoko Zeppelin Sohryu, who in this continuity was not driven insane by the contact experiments, but she emotionally abuses Asuka, turning her into a Shrinking Violet. In an interesting semi-aversion, Kyoko realizes her mistakes when the other NERV personnel nearly murder her for it, and resolves to try to become a better person. She and Asuka are now on at least amicable terms.
Further elaboration; the Grand Highblood and the Condesce went out of their way to have offspring and track them down, against the social norms of their society, specifically so they could do terrible things to them.
In Kill la Kill AU, we have Ragyo's mother, Youko, where this is played straight, in that she even stated she wished she never had her and even forgets her birthday, citing it as the day where her life was ruined. Be noted, Ragyo was six when she said that and it was her sixth, talk about Kick the Dog. Needless to say, after Ragyo is struck by car on that day, her parents divorce, her father taking full custody of her, making that, in his case, an aversion.
In the The Matrix fanfic Bringing Me To Life there's Max's dad, Mr. Jameson, who physically and emotionally abuses his son and wife, along with starving them if he doesn't feel like hitting them.
Kaito Fujiwara's parents. Throughout his life they called him useless and a waste, blamed him for things he didn't do, and constantly held him up to the standards of his older brothers. Not even getting into Hope's Peak Academy was enough to please them, since they considered his talent a waste of time. This treatment is part of what leads him to kill Chiyo. If his animation work was destroyed, then everything his parents said about him would be true.
What little we know about Kumiko's parents suggests this. They're constantly at work, and when they are home they don't even talk to her. She keeps telling herself that it's just because their job keeps them busy, but there seems to be something that's making it harder for her to believe it.
In the Empath: The Luckiest Smurf alternate timeline story "Papa Smurf & Mama Smurfette", the Papa Smurf who married Smurfette is so spiteful to Empath and all his other little Smurfs for expelling him, his wife, and their daughter from the village that he strikes Sassette out of anger for daring to tell Papa Smurf that he stole Smurfette away from Empath, the only Smurf that she sees truly loves Smurfette. Of course, Papa Smurf realizes that he had let his anger toward Empath get the better of him, but it immediately makes Smurfette decide that she's better off without Papa Smurf and so she and the Smurflings leave him behind, with Smurfette taking their daughter with her.
We have this in Kiryuuin Chronicles with Satsuki's step-father when he snatches her out of the closet (where she was hiding the night before) and throws her into a wall. This was after he had beaten her mother and her Parental Substitute.
In Your Servant, Mistress, an all-human fic, Diaval's parents are the explanation for his scars. And Maleficent was raised by her aunt, who emotionally abused her.
Broken Legends's version of Norman is repeatedly described by its creators as an Actual Leaky Trashbag. And with good reason: he's an absolute Control Freak out to browbeat his daughter into obediance. He's done everything within his power to delay her getting a pokemon of her own; 'ideally', he would've preferred she never become a trainer at all, and hoped to eventually find her a partner capable of 'keeping her in line'. The only reason physical abuse isn't a regular factor in his bag of tricks? She hits back. And when she gets cursed to become a Half-Human Hybrid, he gleefully helps turn all of Hoenn against their former Champion, eager for an excuse to keep her locked up the rest of her life.
In The Saga of Avatar Korra while Korra's biological parents are good people, she was kidnapped by the Red Lotus who claimed that her parents were dead, and they would become her new parents. For fourteen years, they subject Korra through psychological and physical abuse in a continuous Training from Hell regiment.
In Ambience: Platoon (Moebius Four) we eventually learn that Franklin's hatred of his parents comes from their attempts to raise him to be a perfect soldier, which frequently skirted close to if not outright became this.
Demigod Power: A number of demigods come from broken homes. Notable examples:
Jolon's mother Jessica, who is revealed to have raised Jolon entirely so she can create a more powerful child from her bloodline. She's also incredibly homophobic and tries to kill Jolon with the intent of replacing him with a Heterosexual clone, so that that one could reproduce in the future.
Koda's mother as well, who beat him severely for most of his childhood.
On the immortal side, there's Phobetor, God of Nightmares, who's a dick to his children and actually rides around in his daughter's mind like a tumor.
Perses, Titan of Destruction, takes away his son's powers and challenges him to prove himself worthy of being his son.
Shirou's mother attempted to kill him more than once.
In Cellar Secrets, this is played with in Ragyo's case. While neither Satsuki or Nui gets the worst of her treatment, she does seem to abuse them psychologically and lorded over them with fear (i.e her beating her secretary and leaving them to see her injuries and the fact that they don't refer to her as "mother"). However, at the same, she was exceptionally cruel to Ryuuko, keeping her caged and isolated in the titular cellar and, apparently, physically abusing her. She does regret her treatment of her daughters and, as she dies, tells them she loves them, however, she acknowledges she can do nothing to atone.
As well, we also have Kermit Clutterbucket who sexually abused Maya and physically beat Katy for trying to stop him.
Edward Bassett is also revealed to be at least verbally abusive towards his daughter, sons, and his grandchildren.
If what Eunice says is any indication about her children growing up to not feel or understand love, then Teddy and Tommy Bassett are possibly just as abusive towards their children as Jennifer is to Farkle.
Claire Ferguson recalls not only her abuse from her father, but also her former husband’s abuse towards her and her daughter.
Morgan mentions that her former boyfriend was at least verbally abusive and would have been physical, if she wasn’t able to fight him back.
The final abuse support group meeting is attended by Eric’s old friend, Jason Marsden who hints that Desiree was abusive as well.
Swordsmen: Akane/Heather's parents, of the neglect and verbal variety, as by her recollection, her mother spent more time drunk than not, and her father couldn't speak a word to her without being overly critical. There's also Morgan Trevor's parents, as her father outright hates her since the only reason he married her mother was because her mother was pregnant with her, plus both of them verbally abuse her, with her mother having outright called her a slut on one occasion. Morgan's mother also forced her to get an abortion the first time she got pregnant, with the alternative being that she'd be thrown out on the street if she didn't comply.
In Children of an Elder God, Shinji was abandoned by his father when he was four and recalled by Gendo ten years later because his father had an use for him. In chapter 7, when Shinji tells Asuka about it, she is shocked and furious.
Shinji, Asuka and Misato's parents. However Shinji mostly pities his father after getting over most of his anger, and Misato has forgiven hers after a fashion... but Asuka wants nothing to do with hers.
In 2025 Asuka's father goes to Japan to try to reconcile with her. Asuka feels tempted to burn bridges with him and salt the Earth, but she decides she will not throw away her chance out of respect for Shinji.
Shinji and Asuka are frightened of parenthood because they are afraid of being this to their child.
In one chapter of The Powerpuff Girls fanfic Ladder, Bubbles is at the hospital to get her blinded eye checked out and decides to try and cheer up some of the younger kids. She meets a boy her age who is bed-bound due to his father beating him up. He beat him so badly that he lost one of his eyes and had multiple lacerations.
Gendo becomes more abusive than his canon self in Thousand Shinji. Rather ignoring his son, he set to break him because he needed him meek and easily manipulable. One of his worst actions was getting Asuka's best friend killed because it'd hurt Asuka, and Asuka being hurt would hurt Shinji.
During his confrontation with Gendo in the twelfth chapter of The Second Try, Shinji summarized everything what his father had done to him and called him out on it:
"What?" he whispered hoarsely, his trembling arms tugging unconsciously on the cuffs around his wrists. "WHAT?? Those words... those words that I had been longing to hear for so long... and you dare," tears formed in his eyes, but he couldn't tell whether from anger or disappointment, "you DARE to say them now? You've never been a father to me. You've sent me away, only called me back to pilot against my will, forcing me through the worst time of my life. Just in the last few hours, you imprisoned me, indirectly threatened to kill me and worst of all used my missing child to torture the woman I love. And you seriously expect me just to be... a good son... and tell you everything you want to know..."
In the beginning of Neon Genesis Evangelion: Genocide, Shinji and Asuka are terribly messed-up and borderline suicidal mainly due to their parent's abandonment and abuse.
In Dark Dynasty, Pan takes the trope Up to Eleven by being an horrible father and grandfather: not only he threw his son away as trash, he also kidnapped his eldest grandson and treated him like prey, refraining from killing him because someone had to continue the bloodline. If you think it's a Pet the Dog moment, he's implied to have sold the kid to dark magic users for wind-wiping and forced rejuvenation because he thought it would be more fun. Nowadays he has ripped his great-grandson's heart to replace his and live forever, and actually plans to abduct his youngest grandson and make him his new toy. Okay, Pan doesn't know about the kid being his other grandson, but you can bet it wouldn't stop him if it were the case.