Being the nice guy and great hero he is, Superman obviously falls under this trope. Especially mess with Conner, Kara or his adopted son Chris and you'll be under a worse ass-beating than usual from Supes.
Also, when Atlas looks over an unconscious Supergirl, who had just been shot by a Kill Sat, he makes a comment that implies that he's going to rape her. Superman's all "HELL NO!" and knocks him into the sky. Sure, Supes would save anyone from that, but Kara is practically his daughter.
Gary Hampton in The Astounding Wolf Man which is fitting because he's in a fact a werewolf. I pity anyone who attempts to harm his daughter.
In at least two alternate universes, Batman has broken or has been really close to breaking his Thou Shalt Not Kill vow when either his adoptive son/sidekick Robin or his protégé/also sidekick Batgirl are in trouble. There is one named The Nail where Superman had not joined the Justice League since he was raised by Amish and not by the Kents, so superheroes were outcasts of society; in that particular world, The Joker kills both Robin and Batgirl in public and very cruelly - this sends the already distraught Batman into such an Unstoppable Rage that he kills the Joker right on the spot and then crosses the Despair Event Horizon. It takes Catwoman and Alfred more than a while to get him at least partially out of his funk.. Another was created when Jason Todd was killed; in this Alternate Universe, Batman kills the Joker, and figures, why stop there? He then proceeds to kill every supervillain in the DC Universe, because he's the Goddamn Batman. The irony? This world, without super-crime and with superheroes able to help with other things now, is a near utopia. And then Superboy-Prime blew it up.
It's not just the Alternate Universe Batmen that fall into this trope. In the regular universe, the only times Batman has come really close to killing occur when any Robin/Batgirl/sidekick was threatened or killed. When Jason Todd was murdered, Batman struggled with the urge to kill the Joker (to the point where Superman showed up to help Batman stop himself from doing anything he might regret later), and the same occurred when Barbara was crippled by the same villain. Then when Black Mask tortured and killed Stephanie Brown a.k.a. Spoiler (who got better), Batman really tried to beat him to death, and was only stopped by Babs endangering herself on purpose. Finally, when Nightwing was almost killed by Alexander Luthor Jr. in Infinite Crisis, Batman grabbed a gun and was about to blow Luthor's brains out at point blank range.
It's kind of a known fact that if you want to grab Batman's attention the best thing to do is threaten the people he works with - especiallyNightwing or Robin. It's the kind of thing the more deranged villains frequently do, e.g. Joker and Two-Face. Papa Bat knows the kids can take care of themselves, but that's not going to stop him from showing up and 'dealing' with whoever dares to harm his children.
Batman was frightfully furious when villain Nobody decided to mock him by making Batman listening to him beating up his biological son Damian. He was prepared to leave Nobody to die in a pool of acid if he hadn't seen Damian watching them and controlled himself in time.
There was also a story where Batman has to do a night of crimefighting while toting a baby around...
Batman: You all know who I am. You know what I can do. But I'm holding a small child here. And if you make me do anything that could possibly endanger this baby... you will be very, very sorry. Forever.
That story ends with the revelation that he was willing to risk revealing his identity in order to give the baby a chance at a normal life with his parents.
It goes back to his father, Dr. Thomas Wayne. The good Doctor was a classic example of The Stoic: in control of himself, logical and not given bouts of emotion. But one night at a Halloween party the Waynes attended (with Dr. Wayne dressed as Zorro and Little Bruce dressed as a skeleton), Lew Moxon needed Wayne's help with an injured man. Dr. Wayne agreed, sewed the man up and calmly informed Moxon that he was going to report the incident to the police the next day. And then, Moxon made an offhand threat against Martha and Bruce. Poor Moxon had no idea he'd just flipped Dr. Wayne's Berserk Button until Wayne decked him so hard his grandkids felt it while shouting, "YOU TOUCH MY FAMILY AND I'LL SEE YOU IN HELL!" It's an awesome case of In the Blood.
Goes so far with Thomas Wayne that in the Flashpoint storyline, he becomes Batman after Bruce is killed in the mugging. Mind you, he's as good as Bruce at the job, but he's probably pushing sixty AT LEAST. It also says something that this Batman is completely willing to kill. In Earth 2, after Bruce dies saving the world as Batman, Thomas become the new Batman and, again, is not afraid to kill.
Batman's fellow crime fighter and Mama BearBlack Canary's boyfriend Oliver Queen/Green Arrow isn't any different. When his son Connor was shot in the head, Ollie forced an arrow between Onomatopoeia's (the shooter) teeth, angrily asking why he tried to kill his kid and just a hair away from making shish-kebab out of his brain. He then decides he doesn't care why Onomatopoeia tried to kill Connor, and tells him that he will die if his son doesn't pull through, holding his bow in that position while the surgeons work. For 30 minutes. With a 200 lb. pull longbow. After giving blood. More recently, poor Connor was shot again (guy has no luck), fell into a coma, and was kidnapped from his hospital bed. Lord only knows what Ollie will do NOW to the ones responsible...
Recently, in the Justice League: Cry for Justice mini-series, the villain Prometheus's plans managed to result in the maiming of Roy Harper and the death of Roy's daughter, Lian Green Arrow's grand-daughter. This results in Green Arrow putting an arrow through Prometheus's brain via his forehead.
Even one of the villainous rogues in Batman, Dr. Jonathan Crane aka Scarecrow, is implied to have tendencies of this. When an Alpha Bitch outright bullies a distraught girl who was one of his patients, he was apparently angered enough to exact revenge on the same Alpha Bitch and her friends by gassing them with the Fear Toxin.
His father the North Wind as well. After spending most of the series acting like a Jerkass God who never seemed to care much for Bigby he sacrifices himself destroying Mister Dark to save his son and his grandchildren.
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.
Let's not forget 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.)
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.
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....
And let's not forget, the whole reason the Punisher has embarked on his waragainstcrime is one bad day in the park with his wife and kids...
"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.
James Howlett akaWolverine is very protective of Kitty Pryde and Jubilee. Too bad his relationship with his biological son Daken isn't nearly as good... since said son is a supervillain. Fortunately, he does have a good (and very protective) relationship with his biological (sort of) daughter, X-23.
It's pretty much tradition for Wolverine to have a female Kid SidekickMorality Pet whom he will fiercely protect. Deadpool actually exploits this at one time to pick a fight with him.
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.
Nathaniel Christopher Summers aka Cable is the trope image, with Hope in his arms for a damn good reason. Hard to believe he used to be an amoral Liefeld character, but Characterisation Marches On.
It carries over to his alternate reality counterpart, Nate Grey a.k.a. X-Man. Don't threaten an innocent around this guy - he wanders up and down the multiverse like it's his personal step ladder and can one shot planets. He's got a nasty temper and he gets creative. He is, after all, Jean Grey's son.
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.
Kaine also shows this trait from time to time when his "niece" is in danger. Must be genetic.
Pretty much 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.
And those that do turn themselves into the police in the vain hope that it will protect them. It doesn't.
Also, a few flashback stories show that his Uncle Ben could be like this too. A former MP in the army, he wasn't a violent man by nature, but was more than capable of getting tough with anyone who threatened his nephew or his wife if talking them into balking down didn't work, as the unfortunate incident regarding Peter's friend Charlie Weiderman proved.
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.
Thabian Polotsk from Gold Digger IS this trope: a super-strong werewolf gentle giant with two young children he would (and almost did) die for.
Adversely, Brendan, another werewolf, disdains his children to the point of homicidal hatred.
And don't forget Theodore Diggers, the father of our heroine(s). He's quick to bring the hurt when his wife or daughters are in trouble.
In a short Ultimate story arc focused on Remy Lebeau, aka Gambit, the mutant finds a recently orphaned girl who immediately clings to him. Resigning himself to looking after her until he can find somewhere permanent for her to stay, Remy quickly grows fond of her. Then Hammerhead, the one responsible for making the girl an orphan, kidnaps her to remove the witness to his crime. Cue completely awesomeRoaring Rampage of Revenge to save her.
In The Mighty Thor, Volstagg is a big, cheerful, friendly fellow, always ready for a fight or a frolic. 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.
Odin was willing to burn the entire world to ash if it meant he could avert the battle between the Serpent and Thor that was fated to end with Thor's death.
Even Loki, of all people, has tendencies to become this whenever his children are concerned (despite the fact that, by his own admission, he has hundreds of children). When one of his daughters was possessed by a powerful agent known as Morwen, well... let's just say it didn't end well for Morwen.
If you hurt someone Thor cares about, then you will truly realise why he is called the God of Storms, because he will bring one the size of a planet down on your head.
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. Of course, 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 Valeria) do have vast powers that make them desirable targets for just about every supervillain out there.
The Thing is this way towards Franklin and Valeria too. In fact, come to think of it, if you really want to make anyone who is on friendly terms with the Fantastic Four very angry, threaten Reed and Sue's kids. It's sure to work.
In addition, Doctor Doom is this way to towards Valeria. He helped Sue give birth to her, and swore than anyone who harmed the child would face his wrath. He is not above using Valeria as a pawn, however. He secretly used an incantation when she was born that would have let him use Valeria as a familiar if the need arose. Her parents were later able to break the spell, but Doom's vow to protect her still stands.
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 pretty much wins too.
Ant-Man II, Scott Lang. Go after his little girl, Cassie, at your own risk. After Doctor Doom kills Cassie during The Children's Crusade, Scott makes it his life's mission to "End Doom."
Towards the end of Enrique Alcatena's Sci-Fi strip Luc Helius the Young Cosmonaut, when the Big Bad corners Luc and gives him a Breaking Speech that sends the kid into an Heroic BSOD... he commits a massive mistake: doing this in front of Luc's beloved father, whom he has been holding hostageand is the reason why Luc embarked in this adventure. The just recently rescued Helius snaps and furiously attacks the Big Bad (who mind you, is a MASSIVE Dinosaur man, and Dr. Helius is a mere human man without any powers), then tells Luc to recover his spirits. This makes Luc react, and he's soon delivering the killing blow to the Big Bad with some help of his True Companions.
A villainous example: The Raider from Paperinik New Adventures:sure,he is a time-travel thief(if of the Noble Demon variety)and he may have several disagreement with him,but the safety of his son Trip is always at the top of his list. He even changed the whole timeline just to find him after he disappeared.
Not quite sure if this counts, but during the Superman/Doomsday: Hunter/Prey arc, Cyborg Superman has Doomsday rampaging across Apokolips. Darkseid heads off to face him (admittedly pretty arrogant, considering this is, well, Darkseid) with a comment that, roughly paraphrased, amounts to "My subjects are mere worms. But they are MY worms, and thus WILL be protected." To put this in perspective, Darkseid has faced Doomsday before and watched him SLAUGHTER his best friend with a look of absolute terror and shock on his craggy face. And Darkseid goes to face him. All to protect his subjects, whom he makes quite clear he really doesn't care about normally. Though, to be fair, he probably assumed that since Superman beat Doomsday, it couldn't be THAT hard.