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.
In Post-Crisis comics, it looks like Supergirl's father Zor-El was a bastard who performed experiments on her and tried to make her a murderer, but it turns out he's actually a nice guy, and it's her mother Alura who is cold, domineering, manipulative and emotionally abusive, to the point she doesn't shy away from using her husband's death to guilt-trip Kara into complying with her orders. In Who is Superwoman? she treats Kara as an incompetent, dumb soldier rather than her own daughter.
Kara: I told you, this isn't my fault! There was a Kryptonian woman— Alura In-Ze: Enough. One more chance. Bring me Reactron. You owe it to your father's memory. [...] I warn you. Do not return to New Krypton empty-handed, Kara. [...] If you pass this test, you will prove to me that you are not as useless a soldier as some would lead me to believe—
Post-Crisis Lex Luthor's father (eventually named Lionel) has at best been characterised as a fellow criminal, and at worst as an abusive, alcoholic monster. In Superman: Birthright, Luthor's father believed he had the next "Einstein" on his hands and was completely ruthless in pushing his son to his creative limits. In The Black Ring, Lex loses it when he finally figures out Superman's identity.
Luthor: I was happy to be rid of what I had for a father! But you...you got them! You're not human! You don't deserve to be Clark Kent!
In Last Son, Chris Kent has good reason to be afraid of General Zod. Zod threatens to put him down along with anyone who stands against him, and fully intends to do it before Superman intervenes. He brushes this off as he "can always make another".
Legion of Super-Heroes: Apparition's absent father in the reboot certainly qualifies, having sold two of her three bodies to pay off his gambling debts. Dr. Londo at least in the Animated Series also qualifies. Timber Wolf's relationship with his father varies on continuity whether he was a bastard or a Papa Wolf. It was assumed before the reboot (in his solo series to be specific) he had a poor relationship with his father when the drug/Zuunium Rays Dr. Londo used on his son was slowly killing him. His reasoning with Gemini/Aria to going into the past (part of her power) which lead to his solo series was in fact to stop his father from beginning the Zuunium treatments which would lead to Timber Wolf's subsequent illness.
Films
In the Superman: Doomsday movie, an adaptation of the Death Of Superman arc, Lex Luthor makes a clone of Superman that quickly gets into Beware the Superman territory. However, he keeps doing whatever Lex tells him, as he was programmed to do—including, in one of his early scenes, just standing there and taking it when Luthor has him walk into a red-sun chamber and then whales on him mercilessly with kryptonite-knuckled gauntlets while screaming out his frustration with Superman for dying and leaving him. Later he has the classic Abusive Parents line "I brought you into this world, and I can take you out of it."
This is all especially chilling because it's presumably what would have happened to the comics character Kon-El, Conner Kent, Post-Crisis Superboy, if Luthor's experiments had run a little more smoothly.
Lex: WHO'S YOUR DADDY?
The clone is all Knight Templar, so he goes rogue from Lex after that, and the first thing he does is dig the kryptonite bomb out of his skull with laser vision (incidentally, apparently the hemispheres of his brain aren't linked?), and then he saves Lois and Jimmy from Lex...and then rather horribly slaughters Lex's incipient clone army, ranging from oversized fetuses to nearly-mature specimens, with the ironic comment "Evil Supermen? Not on my watch!" The line of clones at the stage of development Conner was when he entered the scene were especially nasty to see die, although it was obvious as soon as they were introduced that they'd all have to be massacred somehow.
Lex's dad, Lionel, withholds affection and approval from his son in the warped belief that it will make him stronger. Their tortured relationship is one of the keystones of the series, and ends very badly when Lex kills his dad. It is revealed in Season 3 that Lionel himself suffered physical abuse from his drunken, alcoholic parents, who sought to keep him down in the gutter with them, and prevent him from succeeding at anything; this is one of the reasons he's so oblivious to his abuse of Lex, as he thinks he has a firm grasp of what abuse looks like. And then there's Tess Mercer, whose real parents abandoned her and whose foster father broke her eardrums and arm through physical violence.
In Season 4, we meet Jason Teague, who's parents were also less than loving. His father, Edward, subjects him to Financial Abuse, disinheriting him when he sets off on his own. His mother, Evil Matriarch Genevieve is even worse, being more or less Lionel's Distaff Counterpart. She's emotionally manipulative of Jason and his girlfriend, whom she plans to murder in order to fulfill a prophecy; her control of Jason is so extreme that by the end of the season he's unwilling to do anything without seeking her permission first.
Then in Season 10, we meet Earth-2 Lionel, who is far worse than his Earth-1 counterpart, encouraging his kids to plot against one another for the privilege of being his Bastard Understudy, and eventually tries to have them all killed off at one point or another. Archnemesis Dad indeed.
Western Animation
Dr.MarLondo from the Legion of Super Heroes cartoon series manages to be physically and emotionally abusive towards his only son Timber Wolf. For starters, he performed illegal genetic experiments on his son transforming him into a werewolf-like monster. In Season 2 he implants nanites into his son's brain, driving him insane and uses him to kill a clone of his just so he can get Timber Wolf to work with him again. The sad thing is judging by the photo Dr. Londo showed to the Legion of Superheroes in Timber Wolf's debut episode seemed to imply that he wasn't always abusive.
