Cassandra Cain is an odd case. She received plenty of emotional support and positive reinforcement from the man who raised her from birth to around age eight (who was also eventually revealed to be her biological father), however shooting her until she learned to get out of the way and preventing her from learning language so that segment of her brain would read bodies instead qualify as abuse under any definition imaginable.
Stephanie Brown's father, in addition to being a supervillain, would lock her in a closet when he was angry at her.
Batman himself sometimes dips into this, depending on the writer. All-Star Batman & Robin, the Boy Wonder is the worst offender (the goddamm Batman forces 12-years-old Dick Grayson, age twelve, to live in the cave and eat rats), but it's sometimes seen in the regular universe as well. Bruce can go from the world's best father to the cruelest monster imaginable within 3 issues.
DC comics, Deathstroke/Slade Wilson. Even putting aside how he was heavily involved in the deaths of both of his sons, you could make a case for this solely for Slade's youngest child. Rose Wilson has spent most of her life since her dad discovered her existence trying to deal with his epic-scale emotional manipulations. After rejecting her at first, he stormed back into her life by having her foster family killed and her kidnapped. Then he lured her into being his apprentice and injected her with the same super-soldier serum that gave him his meta-human fighting abilities (crossing over into Physical Abuse as such). Rose eventually had a psychotic break and carved out her own eye to prove her loyalty to him.
Again, crosses over into physical abuse when Deathstroke implants a chunk of kryptonite (which can still give humans cancer) in her eye socket so he could use her as a weapon against Superman.
Rorschach is subjected to this in Watchmen to quite some degree. In a flashback, we see his mother openly providing her services (she's a prostitute) in front of him, and when he wanders in by mistake, driving off her client, she slaps him across the face and says she should have had an abortion. Scarring stuff, indeed.
What he ended up seeing as a kid returns throughout the comic as a pattern on walls, in his childhood drawings, in various shapes (including the shape of his mask at times), and actually is echoed at the very end when Dan and Laurie make the same shadow in a far more peaceful situation. Additionally, Ozymandias ends up alone, casting a singular shadow on the wall in contrast to the double ones shown throughout the book.
Speaking of Laurie, her parents — all three of them — are... not very good at it either. That said, at least two biological ones try. Sally Jupiter does regret their relationship and hopes Laurie will look past the more selfish aspects of her being a superhero stage mom, and the comic ends with her coming to grips with her bizarre parentage, and happily discussing wearing a costume like her father's.
Wally West didn't exactly have the best parents. His father demanded to be given the love that he never got as a child from his family to the point where he (Rudolph West) became the abuser. However, this was actually a retcon, and early comics portrayed Wally and both of his parents as rather close.
Given the level of emotional abuse he subjected her to growing up (his hiding the fact that it was he that sired her upon her supposed harlot of a mother being the least of it) and his leading the mob that shot her and tried to burn her at the stake when her powers kicked in, the above shows that he's nothing if not consistent.
When Harry Osborn got his first bike, some boys stole it from him. His father took it back only to break it into pieces in front of his son and tell him that this is what happens to the things that he can't guard. Years after, because of his toxic father, Harry started to use drugs and it is part of the reason why he became the second Green Goblin. And what Norman went on to do makes him king of this trope.
In American Son Story, we learn Norman had sex and knocked up Harry's current girlfriend and made Harry think it was him. Worst father ever? You decide.
Norman's own father was also abusive to him. It must run in the family.
While Harry was going insane as Green Goblin II, it was heavily implied that he was grooming his son to be just as much of a maniac as him, but it never seemed to be physical.
The worst part is that the combined (perceived) hate of Spider-Man and his father was fully responsible for Harry becoming the Green Goblin again and leading to his death — and that it was all his own imagination.
Mary-Jane's father blamed his family for his own failed ambitions, and is generally depicted as a deadbeat, often-alcoholic trainwreck. In the 2000s film trilogy, she's clearly desperate to get away from his verbal and emotional abuse, and he only shows up at her plays to ask for money.
Oh, and there's Black Tarantula, Spider-Man's ex-enemy, who, in the '90s, tried to take his son from his ex-wife, both of whom were under the protection of another criminal. He attacked that criminal's headquarters alone and defeated everyone who got in his way, including Spider-Man. However, when his ex-wife reminded him how his father had destroyed his childhood by forcing him into training and asked if he wanted the same for his son, he just walked away, leaving them alone.
One of Ben Reilly's girlfriends, Elizabeth Tyne, who decided to become a Self-Made Orphan. Made worse in Spider-Girlof all universes, where it's implied that after turning herself in, Elizabeth spent the rest of her life in prison for killing the jerk. Oh, and her son ends up being (physically) abused by her family, too.
Howard Stark, Tony Stark's father, was verbally and emotionally abusive. As a child, Tony respected his father greatly and wanted to please him. However, in spite of Tony's genius, Tony's reluctance (and inability) to assimilate his father's "ethics" caused Howard to resent and despise his son. Howard's rejection hurt Tony deeply, and although Tony has long since lost all respect for his father, he's never entirely gotten over it, as shown in Iron Man: Legacy of Doom:
(in Mephisto's Realm, Howard Stark's spirit appears before Tony) Tony: Y-you? Howard: Losing again, eh, boy? You always were a wimp. Never had the stones to do what had to be done. Tony: I always tried to do what was right! Howard: Brilliance isn't enough. You'll never reach your true potential worrying about consequences. You're weak.. [...] You're no son of mine. Tony:I'd heard it all before. But the pain was still enough to distract me from the physical task at hand. (Howard lunges; Tony flees, unable to attack his own father) Howard:COWARD! You were my greatest shame, but I'll make a man of you yet! I'll beat it into you! (later, after Howard is defeated) Tony:You can't kill something already dead. I'd been telling myself that for a long time.
In Legacy of Doom, Howard is also physically abusive, but it's unclear whether or not Howard ever physically abused Tony in life. (Although Tony doesn't seem too surprised by Howard trying to kill him; but then again, Tony is in hell.)
Howard makes Tony to drink a cup of bourbon when he's a child in order to win some momentary approval. He may have not forced it down Tony's throat, but he did coerce Tony into doing it, and that transcends into physical.
The Secret Origin of Tony Stark seems to have given a major reason to all of this - stress due to the fear that the Rigellian Recorder would realize that Tony wasn't his true son, that he was adopted to save his biological son, Arno, from being used as a weapon. Tony... is still mixed about the whole thing.
When Knuckles was born, his parents soon begin arguing about the proper way to raise him. It eventually got so bad that his father Locke divorced his wife and took sole custody of the boy so he could raise him to be a guardian. Locke essentially abandoned his son when he was ten years old, forcing him to fend for himself for years with little or no contact with other people. Locke insists that all of this was done to build character and make Knuckles a better guardian by forcing him to do things himself. In truth, he had Knuckles under close observation the entire time he was "abandoned" and often expresses regret at causing his son so much grief, but he still insists he was only doing his job. However, Locke did get a considerable comeuppance, as his actions regarding Knuckles led to an echidna scientist going rogue and getting a considerable number of their race slaughtered.
It may run in the family. In an early issue of Knuckles' spin off series, Knuckles talks to his mom about why the family broke apart. In the ensuing flashback, she talks to her mother in law about how she felt when Locke was taken away for guardian training. Said in law paused and only said that she'd be lost without her husband.
In the Continuity Reboot universe, the abusive parent here is now Rotor's father, who seemingly hated Rotor's amazing genius and inventions. It got to the point where Rotor ran away to Mobotropolis (arriving just after Eggman took over) and Rotor's father became an Egg Boss.
Squee!'s dad openly despises him and often talks about how Squee's birth ruined his life, Squee's mom is too drugged out to remember she has a son half the time (the other half she believes he's already grown up and moved out.) The series ends with them signing him over to a mental hospital for experimentation.
Jason Rusch's Firestorm (pre-reboot) was physically abused by his father.
The very first time we see Chase Stein of Runaways, his dad is punching him in the face for getting bad grades. It's implied that this sort of thing has been happening regularly for most of Chase's life, and as the series goes on we find serious issues under the Book Dumb jock facade. He eventually admits that he convinced himself there must be something wrong with him to justify all that, and suffers from Multiple-Choice Past as a result. He can't quite tell which bits are the lies he told himself anymore.
Later on, the group adopts Klara Prast, a Swiss immigrant from the early 20th century whose parents declared that she was wicked because of her strange powers, and thus sold her into marriage to a creep who repeatedly raped her, sent her to work in unsafe factories, and threatened to sell her into outright slavery if she complained. And this was when she was only goddamned eleven years old.
Marvel Comics' Tabitha Smith/Boom-Boom was abused by her father until she ran away from home. This is a pretty commonplace trope for their mutant characters.
Brenda from the Jaime Reyes Blue Beetle comics. Her father reportedly knocked her around on a regular basis at first, but then upped the ante and put her in the hospital when the police questioned her about Jaime's disappearance, causing Brenda's crime boss aunt to have him killed.
Marvel Comics' Bullseye possibly has an abusive father. Whether it's true or not, the guy is dead.
Psychologist: And you say your father beat you? Bullseye: Yes, until I was fourteen. Psychologist: Hmmm. I see. And what happened then. Bullseye: (kills psychologist with a voice recorder) I killed him.
His mom apparently wasn't too great of a woman either.
Bullseye: (as he becomes a Dark Avenger) Pity I killed my mom in high school- she would've loved this. (beat, as everyone stares at him) Kidding. She wouldn't've cared.
Carnage, another crazy supervillain from Marvel, has serious issues with this. At least one of his parents was abusive. He said once that his mother tried to kill him, but his father saw this and killed her. However, another time he said that his father killed his mother, when he was trying to kill him. Possibly his grandmother was that same kind of person. For both father and grandmother it didn't end well.
The Flash villains Captain Cold and his sister, the Golden Glider, were abused by their father. Years later, Cold had the chance to kill his dad, but couldn't bring himself to do it and let Heat Wave do the honors.
In a Back Story, Bull Bushka (the former school bully turned physical education teacher) reveals that he was physically beaten by his father ... hence, the reason why he tormented the strip's main protagonist Les Moore all these years.
Other storylines have seen Susan Smith (the girl who had a crush for her teacher, Les, and maintained it as she became his colleague) being beaten by her boyfriend while in high school; and Lisa Moore (who was beaten by her one-time boyfriend, the one that got her pregnant as a teenager).
The DCU's Damage was sexually abused by his foster father.
According to Elektra: Assassin, Elektra of Daredevil was sexually abused by her father at the age of 5, after which she was told it had never happened until she more-or-less believed it.
Dead Irons: Meet Devin Irons, the father of four children, whom he severely abused and then offered as souls in a pact to a Plague Bringer Demon for the power to control human minds, turning all but one of them into soulless, vicious monstrosities intent on bringing death and destruction to the Old West. He killed Silas Irons only father figure after he came to confront him for tying his son onto a statue, bloody and beaten, and painting "sinner" onto his chest. His crowning moment of assholeness comes when he brings his own wife, now a mindless flesh-eating ghoul, back to life as a lure to bring his adult children back to complete a ritual that will make him immortal.
Then there's Bruce Banner's father, Brian. He'd been abused by his father, leading Brian to believe his father was a monster, that he had inherited the 'monster gene', and that any children he had would be monsters too. Brian initially chose to ignore Bruce, believing him to be a monster in the making. When it became apparent Bruce was a child genius, Brian saw his worst fears confirmed, and started beating both Bruce and his mother, Rebecca. After several years of abuse, Rebecca attempted to escape with Bruce, but Brian killed her and intimidated Bruce into saying Brian hadn't done anything to them. The truth only came out when Brian got drunk and boasted about what he'd done. Brian was locked up in a mental institution, dying shortly after release. End result? Bruce developed multiple personality syndrome - and after a certain accident with a gamma bomb, his personalities became the various Hulks. And Bruce (accidentally) killed him. In a subsequent story, Banner himself admits it might not have been accidental. He's back from the dead and in Devil Hulk form in the Chaos War tie-in.
Darkseid is all over this trope. He has 3 known sons, all of whom he treats badly to various degrees. He feels nothing but contempt for Kalibak, ignoring, mocking, and blasting him with Omega Beams whenever it suits him. His other son Grayven is an outcast. Oddly enough, the son Darkseid favors most is Orion, the one he sent away to be raised by his enemies. This didn't stop Darkseid from killing Orion in the opening of Final Crisis.
Felix Faust manages to be the worst father in comics with one act: selling his infant son's soul to a demon for power. Luckily (well, sorta), the demon Nebiros decided to screw over Felix and gave the kid the power instead — after taking the soul. Turning your own son into a soulless abomination of the universe in a selfish bid for more power takes abuse to a whole new level.
The Red Skull from Captain America may be the worst father in comics. When his daughter was born he tried to throw her into the ocean because he didn't want a female heir. He was convinced to allow her to live by one of his servants, but demanded she be raised without love. Skull treats her more like a servant than a daughter, heaping emotional and physical abuse whenever he can. Also when his daughter was injured on a mission, the Skull seemed not care about the welfare of his daughter, instead finding the situation amusing. Even worse, he used a machine to Mind Rape his daughter in order to "educate" her.
Norbert Sykes, alias The Badger, was beaten, saw his dog shot and was eventually raped by his stepfather Larry. This left him with multiple personality disorder, a violent streak a mile wide and an obsession with the name Larry.
Jonah Hex's father Woodson Hex abused his son both emotionally and physically and ultimately sold him as a slave to the Apaches.
The retellings of Two-Face's (i.e. Harvey Dent's) origin have this present, largely being physical with an emotional element. The origins of the "Two-Face" persona come from a twisted game Dent's alcoholic father would play with him, based on a coin toss; heads, Dent's father would beat him senseless, tails, Dent would be off the hook. The catch was that the coin was a double-headed one, and Dent never won. The idealistic part that hoped the coin would land tails one day would go on to be Harvey, while the cynical part that knew it never would became Two-Face.
In the IDW incarnation of the Teenage Mutant Ninja Turtles, Casey Jones' father is one of these. In fact, it is the very first thing the reader finds out about him.
Irredeemable: Tony was originally found by a broken woman mourning the death of her child that she had just accidentally let get killed. And she would repeatedly try to kill Tony in various other ways, failing because Tony is a Superman expy, and really even then didn't know what was going on until finally trying to go for Pater Familicide in the garage.
His later parents, the Hartigans, put him through Training from Hell, which all-in-all wasn't that abusive; however they teach Tony to never use his powers for the benefit of himself or his family, to the extent that he was never allowed to fight back against those who bullied him. When Tony off-handedly mentions that he saw a brain tumor in his mother's head, the Hartigans' anger reveals their hypocrisy and, in an event that scarred Tony for the rest of his life, committed suicide hours after finding out.
It was hinted that Loki's biological parents were neglectful and downright abusive. He managed to get his revenge, though.
Loki: You will never strike me again! NEVER!!!
Baron von Strucker viewed two of his children, the twins Andreas and Andrea, as worthless disappointments and wasn't that shy about that fact. His reaction when Norman Osborn tells him he killed Andreas? That the baron owes him a favor. And he himself killed his other son Werner as part of a HYDRA power struggle.
ElfQuest has Winnowill, a powerful healer who imprisoned her son in a cage and used her abilities to torment him, eventually splitting his mind in two and driving him mad. He gets better, mostly. She refuses to.
Ninjette's alcoholic father in Empowered. Physical violence, check. Constantly verbally abusive towards his talented daughter, check. Wanted to marry her off as a virgin bride to have lots of ninja babies, check. Murdering the prince of the allied clan that Ninjette actually lost her virginity to (starting a war in the process), then displaying the prince's dripping head to his wayward daughter as an example... uh, check.
Zipi y Zape: Played for Laughs. Mr. Pantuflo has no trouble in brutally beating the twins or locking them in a mice infested room with no food or water. Even worse is the fact that this is seen as normal.
Mr. Pantuflo, in the later Escobar strips (the ones which are mostly available), is a saint in comparison with his incarnation in the older, black and white ones, in which he punished his sons with incredibly brutal and sadistic penalties, such as crushing them with a huge steamroller, tying them to a bed of spikes with a large and scary boulder over their head or abandoning them in the middle of the sea. By far, the most disturbing of all is one strip in which Mr. Pantuflo puts them on a guillotine with a basket at the bottom to collect their severed heads.
The same happened in the first color ones. Punishments included throwing them into a lion-infested room, sending them packed into a satellite to the stratosphere, or fusing both brothers into one, so Pantuflo would always know who did all mischiefs.
X-23 can certainly fall under this trope depending on how you define "parents." Zander Rice was one of the lead scientists involved in her creation, and the abuse he leveled at the poor girl was outright horrific. Her mother, Dr. Sarah Kinney, (who provided the surrogate womb and some genetic material) was under the orders of Rice and project leader Martin Sutter to deny X-23 an emotional connection. To her credit, though, Kinney defied those orders whenever she could, but couldn't prevent the emotional damage the young Laura sustained before she could be freed from the Facility's control. And let's not even get into what Kimura, her other primary adult "role model," did to her...
Hints dropped throughout Innocence Lost (including a copy of an actual police report) and Target X reveal that Sarah herself was abused by her father, which neither her mother nor sister would corroborate, ultimately resulting in Sarah cutting off contact with her family and only briefly reconnecting with her sister before her death.
Kimura was also the result of a neglectful mother and abusive father. Her grandmother attempted to undo the damage, but by then it was too late, and Kimura used the abuse and bullying she suffered as a child as an excuse to do it back to others when she grew older, particularly Laura.
Hummingbird, a she-villain from Hawkman, had one of these in the form of a super-fanatical Granola Girl. The most well-known thing about Hummingbird's mom is that she stabbed Hummingbird's father 47 times, killing him in the process, for the "crime" of cooking pancakes for himself and Hummingbird. Hummingbird's eventual response was to tie mom up in bed and then burn her to death. It's unclear if she was awake or not at the time, though.
The Joker has made claims of having one or more abusive parents to his various psychiatrists before in pre-New 52 continuity, most notably when he corrupted Harley Quinn, but even he isn't sure if he's telling the truth or not when he does. In New 52 continuity, it's been implied he genuinely did have one, in the form of a highly abusive aunt (she starved him, beat him, and washed his face with bleach regularly)... who knows if that will or won't remain canon, though.
Wolverine from the X-Men had an abusive mother. Elizabeth Howlett Hudson was neglectful of her son as she became mentally ill after witnessing her first born son John's claws emerge for the first time, leading to her scarring (her absences were to the asylum); in her few visits to the Howlett Estate she wasn't seen interacting with James. However after history repeated itself with her youngest son (who had just witnessed his step father murdered and had just slain his biological father in his rage), her response was to smack her son across the face with her lover's rifle and disown him, calling him an 'animal' as he fled the estate.
His biological father was never a saint; he regularly beat and abused his son, Dog, and introduced the boy to alcohol while encouraging the boy's sociopathic tendencies.
Lian Harper's mother Cheshire is an emotionally abusive kind. She initially had Lian for the sake of tormenting Roy Harper after he walked out on her, intending to taunt him with the fact that he wouldn't know what his child looked like, her name, or her gender. When Roy gained custody of Lian, this started a trend of Jade consistently disrupting their lives and using her position as Lian's mom to exert some control on Roy. It finally reached a point when, during her stint in the Secret Six, Jade conceived a replacement child when Lian's well-being was exploited to make her stay on the team.
Emma Frost's father was cold and emotionless and encouraged his children to play mindgames with each other. Her mother was a neglectful drug abuser.
Reginald Hargreeves from The Umbrella Academy. He would chide his adopted sons and daughters if they called him 'Dad'. In one story, he sicced a murderous supervillain on The Rumor when she lied about sneaking out for the night to see a boy. Jerkass doesn't begin to cover it.
Vanya: "Dad.. ? I mean, Mr. Monocle, sir? Why can't I play with the others?" Reginald: "Well number seven... there's just nothing special about you." Vanya: "Oh."
In a flashback in Knights of the Dinner Table, it's heavily implied that Brian's father was verbally (and probably physically) abusive to him. The scene consists of poor 12-year-old Brian cowering against the wall in his room, surrounded by toys, games, and assorted geek paraphernalia, while his dad shouts at him for his poor grades, and "living in a dream world." All Brian can do is feebly mumble, "Y-yes, sir," causing his father the shout "ARE YOU LOOKING FOR THE BACK OF MY HAND?" No wonder he prefers fantasy to reality.
Stanley and His Monster's appearance in the Green Arrow arc "Quiver'' sees Stanley's grandfathter and namesake as this as he was a Satanist who wanted to sacrifice his first born infant to a demon to gain immortality and he wasn't any better to his grandson and began to starve and torture Stanley. This culminated in Spot, the "Monster" of the duo, giving Stanley Sr. a well-deserved death and mindwiping Stanley to save his sanity.
Gary Richards. It's no wonder Reed turned out so mentally unstable. Gary is from the first issue shown to be verbally and emotionally (if not physically) abusive toward Reed, having no interest or tolerance for Reed's tinkering, yelling at him for turning the phone into a device, then throwing it at Reed's dinner. A later issue suggests Gary was physically abusive as well. Thanos manages to torture Reed by conjuring an image of Gary prepared to beat him.
Thanos to his three children. He physically abused Ronan to make him subservient, and removed all the skin from his daughter's arm, just for talking back. Hearing Atrea trail off describing his parenting style causes Ben to remark that he sounds like Reed's father.
In Young Justice, Arrowette's mother is a former superheroine-turned-Stage Mom who tries to force Cissie into taking up her old mantle so that she can vicariously relive her "glory days". While Cissie eventually forgives her, she also makes a point of not living under her mother's roof.
Wolverine's archenemy Sabretooth had an abusive father... Possibly, given all the screwing with his memory as part of the Weapon X program. Part of Sabretooth's mutant powers is his canines growing into fangs and fingernails into claws. After his powers manifested, his father chained him up in the basement and pulled those out with pliers. And since rapid healing is part of Sabretooth's powers, they had grown up by the next day, so his father repeated it again and again and again and again... And as sadly tends to be Truth in Television, Sabretooth himself grew up to become an abusive parent in his own right to his son Graydon Creed, which helped fuel his hatred towards all mutants.
The man who Wis' mother was betrothed to never forgave her for bearing a child that wasn't his, and took it out on Wis once she died. Wis eventually kills him by hacking off his fingers and throwing him off a castle tower.
Ghorghor Bey's stepfather wasn't any kinder to him, largely because Ghorghor was the result of an ogre raping the woman he was in love with during an attack on their mountain village. He stayed his hand from killing Ghorghor at birth because of his mother's pleading, but after she died he threw out Ghorghor for good. Ghorghor, finally fed up with the years of abuse, kills the man before leaving the town.
In Shazam!: The New Beginning, Dr. Thaddeus Sivana is this toward his two children Beautia and Magnificus, and also to his nephew Billy Batson, whom he was given custody of so that he could inherit the boy's life insurance from his parents in order to fund his research.
In Plutona Ray's father is a neglectful unemployed alcoholic.
Bertron, the alien scientist from Superman/Doomsday: Hunter/Prey, is this of the creator/father sort in that he subjected his creation, the creature that would someday become Doomsday, to a constant cycle of death and rebirth in order to force evolution upon the child so that he would grow to become the Ultimate Life Form. Upon reaching that goal, however, Bertron found himself at the mercy of his own creation as it turned its attention toward its creators after killing all the resident lifeforms on the planet. Bertron tried to talk down the creature by saying, "You cannot kill...your own father," only to be killed soon afterward. Years later, Waverider would find out that the creature's rampage is fueled by the fact that it sees everything it comes across as a reflection of its creator/father.