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
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)).
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.
Queen Of All Oni: 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 arent 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.
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.
In the Horseshoes and Hand Grenades story, Wheel of Fortune, Mei Shirakawa suffers from parents who don't really care about the situation with Yamada Tatsumori, and when she was sent to the hospital, they screamed at her for being so careless. In fact, when Mei went to the hospital to check on Jiro, her mother left her behind. It's later revealed that this is because she failed to do a proper ritual and her parents were unable to claim the special inheritence from it. Needless to say, when they died no one cared.
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. She emotionally abuses Asuka, turning her into a Shrinking Violet, rather than the Jerkass that Asuka was in the series. 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.