Rick Grimes in The Walking Dead will do almost anything to protect his son Carl.
When a couple of bandits attack them on the highway, one of them attempts to rape Carl while another restrains Rick. Rick RIPS THE BANDIT'S THROAT OUT WITH HIS TEETH and proceeds to mercilessly stab the other to death.
During the arc "The Long, Cold Dark," Castle's vengeful nemesis Barracuda targets the Punisher by kidnapping the daughter he unknowingly had with Kathryn O'Brien. When Castle finds out, he is pissed, to say the least, and at one point he spends an hour running electricity from a car battery through Barracuda's genitals just because.
The beginning of the comic, when Barracuda actually gets the drop on Castle and handcuffs him to a chair, then reveals his daughter and holds a knife to her (and trust us on this, Barracuda was going to torture her to death for the sake of revenge). Frank goes into Unstoppable Rage and has to piece together the following events by examining his injuries in a hospital bed. (He snaps his wrist in a heartbeat to get out of the chair, lunges across the room and tears a chunk out of Barracuda's cheek with his teeth. If 'Cuda hadn't thrown him out the window, he would have torn him limb from limb.)
Another Punisher MAX moment. In the story arc "Mother Russia", Castle is charged to rescue a little girl from Russian bad guys (to put it brief: There's a big plot about germ warfare). Upon entering the complex where she is held and meeting her, he says "My name is Frank. If anyone else tries to be mean to you, I will be much, much meaner to them. I promise." Soon after, a skinny, half naked Asian super agent comes and kicks the crap out of Castle with the butt of an AK-47. In a daze, he sees the agent slap the girl. He gets up. The agent throws a kick. Castle grabs his ankle, twists and slams him against the floor, walls, and ceiling until the agent is a pulpy mess and twists his leg off "like a drumstick." Do not fuck with kids around Frank Castle.
Even then, the only reason he stops is because he's scaring the kid.
And yet another MAX moment. Castle is conversing with one of his hooker informants. He's glaring at a pimp, who's guarding over a young girl. He asks the hooker how old the girl is. She says she's about 13 and mentions drugs. Castle walks to the pimp, pulls him into an alley, and emerges from the alley alone.
Punisher: Tell the new guy to behave himself. [walks off] Old hooker: ...that was not my fuckin' fault.
"Kitchen Irish" features a Grandpapa Wolf in Napper French, a retired mob cleaner and the best of his kind. French was legendary for his ability to pull a "Houdini" on a body, to make it disappear completely off the face of the Earth. Irish gangster Maginty kidnaps Napper's grandson to force him to pull one last Houdini...on a live man. He has no choice but to comply, but near the end of the job, Maginty, for his own amusement, shows Napper's grandson what his grandfather had been doing, traumatizing the young child. So Napper decides to give Maginty a firsthand demonstration of how one pulls a Houdini....
The whole reason the Punisher has embarked on his waragainstcrime is one bad day in the park with his wife and kids...
The MAX arc "The Slavers" is another Papa Wolf moment for Frank. Encountering some human traffickers, Castle is so enraged with what these scum do to their victims, that by the end of the arc, he's shocked at what he has done. Including carving up one of the ringleaders, wrapping his intestines around a tree, and then waking the man up.
Even villains can fall under this trope. When Marvin and Wendy suffer their utterly ridiculous, cruel, and pointless death and maiming respectively at the jaws of a demonic Wonder Dog while working with the Teen Titans, their father The Calculator is somewhat understandably pissed. Being a villain, he acts as a very dark Papa Wolf. His vengeful scheming has already claimed the life of Eddie Bloomberg aka Kid Devil. He's even gone so far as to search for the Anti-Life Equation in the hopes that it could restore Wendy's ability to walk. It didn't work out.
Similarly, Deathstroke, Slade Wilson, father of three, who took up a personal vendetta against the Teen Titans when one of his sons died fighting them. His other children, Rose and Joseph, meanwhile, instead joined the group. He's an action dad, but a terrible father non-the-less.
Nathaniel Christopher Summers aka Cable, after adopting Hope Summers, is this nowadays, and a rather good one too. Hard to believe he used to be an amoral Liefeld character.
Cable's pap Scott Summers too, while not the best dad, he did his best to take care of Nathan (even spending his honeymoon in the future taking care of him because he missed the chance to do so in the present), but he was kinda busy with work. What was his work? Being the leader of the X-Men, that's what.
Marv from Sin City is like this to the girls at Kadie's Bar, especially Nancy. Granted, it's due to his enormous chivalry, but given his age and the ages of most of the dancers, I say it counts. He mentions one moment when a frat boy roughed up Nancy, which hit his Berserk Button about hitting women in general, and he "straightened him out but good," mentioning that he maybe went a little too far (implying that the other guy didn't survive). There's also the short yarn "Silent Night," where Marv hears about a mother asking after her missing daughter, then hunts down and kills her abductors (who had been planning to sell the poor girl for sex) and cradles the terrified child in his arms in a rare tender moment before taking her home.
The corrupt police commissioner Liebowitz turns against the Wallenquist crime organization in "Hell and Back" after his Dragon The Colonel orders the assassin Mariah to break Liebowitz's son's arm to remind Liebowitz of the organization's power over him. Liebowitz responds by organizing a police raid on the organization's human trafficking operations. Then he personally blows The Colonel's brains out and orders his officers to "make a missing person out of the fucker."
Luke Cage: Hero for Hire: Norman Osborn learned the hard way to not endanger Luke Cage's girlfriend (now wife) Jessica and their (then unborn) daughter - Luke beat the tar out of him in public, not caring if his already revealed identity took a nosedive in regards to reputation.
Osborn himself, though in recent years he's more likely to strap a bomb to his kid and use them as a human shield than he is to protect them, but the original reason he truly came to hate Spider-Man, and why he killed Gwen Stacy, was because he blamed him for his son's second drug overdose, one that nearly killed him.
Kaine also shows this trait from time to time when his "niece" is in danger. Must be genetic.
Every incarnation of Peter Parker has this to some extent.... Granted, most versions don't have children, but they all have a big blinking button somewhere in their psyche labeled 'someone hurt my loved ones', and the majority of the New York underworld can tell when some idiot has pressed it.
Hint: the reason the motor-mouthed superhero hasn't talked in the last sixty seconds is because he's using all his superior intellect and enhanced nerve conduction velocity (IE: ability to think faster than normal) to consider the merits of the 6,000 different ways he intends to hurt you.
There's also ASM #645. He's led to believe an infant he was trying to protect is killed. He then proceeds to go on a rampage. It's so bad, that some of his rogues gallery don't believe it...until he comes for them.
Scandal Savage and Bane of Secret Six have something of a father-daughter relationship, with Scandal's biological father being... well, VandalSavage and Bane being a Genius Bruiser when not on his venom, and it seems the one surefire way to get Bane to use said venom again is to put Scandal in danger, at which point anyone who happens to be in the way gets to experience what the Batman went through in Knightfall — that is, a broken back.
Volstagg in The Mighty Thor. Harm, or even threaten, any of his children, biological or adopted, and he will come down on you like the wrath of the angry god he is. IT doesn't need to be his kid either, he'll take you out for harming any child near him.
A rather twisted example would be Sinestro. Harm his daughter, Soranik Natu, and you will have the wrath of the entire Sinestro Corps bearing down on you and your entire planet, as the Weaponer of Qward learned. Being Sinestro, this happens after he lets his daughter's boyfriend, Kyle Rayner, fail in a rescue attempt first just to show her how unworthy he is.
Reed Richards, along with his Mama Bear wife Sue Storm, of the Fantastic Four, especially given that both their children (Reality Warper Franklin and Child Prodigy Valerie) do have vast powers that make them desirable targets for every supervillain out there.
Ultimate Howard Stark. Who, for the occasion, had come prepared with a 26-man SWAT team and a team of paramedics, all of which he had (presumably illegally) bribed to do his personal work. "Exactly where is my boy, and how many people do we have to kill to get to him?"
The assassin Deadshot aka Floyd Lawton, on-and-off member of the Suicide Squad (and one of the few good enough to survive multiple stints on it) and member of the Secret Six (pre-Flashpoint). In one storyline he discovered that he might have fathered a daughter. When he visits the mother Michelle (a former prostitute and junkie who cleaned herself up for her daughter's sake) he sees his daughter for the first time, an adorable little four year old girl named Zoe. He wages a one-man war against the three crime families fighting over their neighborhood just so Michelle and Zoe can have a better life. He wins too. He later finds out he has another kid to boot.
Ant-Man II, alias Scott Lang. Go after his little girl, Cassie, at your own risk.
Similar to Scott Lang, DC's Roy Harper, AKA Speedy/Red Arrow/Arsenal, who fathered a daughter with the super-villainess Cheshire, one who he was VERY protective of. When they disgustingly killed her off, Roy went a bit nuts.