Kenzo Kabuto from Mazinger Z and Great Mazinger. It is arguable if he wasor was nota good father. It is not arguable when his older biological son was about of being killed he sent a Humongous Mecha after the people was attacking him, and when his adoptive son was about of being killed, he blew his assailant and himself up. Therefore, althought his parental skills left much to be desired, you DON´T try to hurt his sons.
Henry Maaka from Karin is usually a weak-willed wuss, but when his daughter Karin is in trouble, he will let himself burn to rescue her from the hospital people who think she's an Ill Girl, but could potentially discover that she's a vampire.
Most people try to kill vampires with stakes. Henry uses uprooted trees.
Takahata is this way as well, but to Asuna in particular he's an adoptive father. Although only because his self esteem is too low to be her boyfriend.
Oga from Beelzebub seems to not care for Beel, but, if you put a finger on the baby...
In chapter 107 he openly declares himself to be Beel's parent, emphasizing this trope even more.
Whenever he learns that his daughter Ran Mouri and/or his charge Conan Edogawa are or have been in danger, Detective Conan's KogoroMouri is definitely not pleased. And you do NOT want to provoke a man who looks and acts like a slob, yet is a National-level judoka andacts at his most competent when It's Personal. More than one suspect has been at the receiving end of a powerful judo throw for this.
One Piece has Garp, Luffy's gradfather and the father of Dragon The Revolutionary.
Also, Luffy's actual father Dragon the Revolutionary has appeared only once or twice, but one of these apparitions puts him squarely here. When Luffy was about to be arrested by Smoker...Dragon shows up and keeps him from using his weapon. Then a gust of green wind blows through the island, freeing Luffy from Smoker's clutches. It hasn't yet been revealed if the wind was Dragon's doing, but...
In the second OAV based on the video game Fatal Fury, titled FATAL FURY 2: THE NEW BATTLE, lead hero/fighter Terry "The Wolf" Bogard has lost his will to fight and live after being beaten by Wolfgang Krauser, only to have a street kid named Tony tag along with him. Tony, who lost his father in a street fight and works as a shoe shine-boy to support his mom Elsa, worships Terry's reputation as a fighter and wants to be his disciple. After the defeat, Terry spends half the special getting drunk and not caring about anything... It is only after Axel Hawk, the heavyweight boxing champion of the world, orders his sparring partner to beat Tony within an inch of his life in a bar (after Terry drunkenly refused to fight Hawk when challenged), does Terry rise out of his funk...and drops Hawk with ONE PUNCH. Even Hawk can't believe it (as his inner narration mentions).
In The Movie, Kim Kaphwan gets to show off his Papa Wolf credentials as well. When a Brainwashed and Crazy Cheng Sinzan steps into a party he's attending with the main cast and his family, Kim offers to fight him so his two kids can see him kick ass. His rival, however, soon starts wiping the floor with him, so much that Joe has to be stopped by Andy from breaking in... but the very moment one of the Kim boys begs his daddy to not lose, Kim brings himself back and completely curb stomps his enemy with a single Ho-oh Kyaku.
Despite being the hero of Lone Wolf and Cub, Ogami Itto averts this trope - if anything he's an Underprotective Dad. Mainly because his toddler son Daigoro is a samurai too, and though he he does love his kid... if he should be killed, that's a risk that comes with the job.
However, Ogami has pulled more than one You Shall Not Pass for his clients either in the process of getting the job done or to repay a debt of honor: once, he stopped by a village whose men had all been drafted for war and helped them till a field, even to the point of cutting down anyone who tried to pull him away, because he'd been asked to do so by his last assassination target.
Despite being the youngest (male) of the group, Mobile Suit Gundam 00's Setsuna F. Seiei is quite the Papa Wolf for his teammates in season two. This is so pronounced that sensing his comrades all on the brink of death pissed him off to the point that he unknowingly initiates the "Trans-AM burst mode", completely turning the tide of the battle.
An ironic example is Sergei Smirnov, who has been called ''Papa Bear'' (because in-universe he's nicknamed "the Wild Bear of Russia") by fans with the description of Papa Wolf in mind. He did fit the Papa Bear description given above regarding his treatment of his son Andrei, but with Soma Peries he was Papa Bear all the way.
The battle on the moon: Spirit may be a womanising twit, but he isgood at his job, and pulls off another Big Damn Heroes moment to protect Maka from Crona.
Fairy Tail: Macao Conbolt. After the timeskip, Alzack Connell also becomes one.
Don't so much as think of threatening Pinoko or Black Jack will cut you to ribbons. Then sew you back up. Then charge you everything you're worth for the trouble... Yeah, it's just that kind of story.
While not a biological father, Sousou/Cao Cao from Ikki Tousen is this towards his friends. So much, that his Superpowered Evil Side took full control of him whenever he saw them in danger. It first happened with his Unlucky Childhood Friend Chuukou (he thought the bullies at their judo club were attempting to rape her), and later with his Bash Brother Kakouton (who lost his eye while shielding him)). And in the anime series, he also recruited Myousai by protecting her from a rapist and offering her a chance to be his subordinate and fighter instead of a Child Soldier.
They may have marital problems in Macross 7, but don't ever think of threatening any of their children or their city or their ship; coz when Mama Bear Milia and Papa Wolf Max Jenius team up, you are definitely screwed. Especially emphasized on their killer combo attack in Super Robot Wars Alpha 3 as seen here.
Minato Namikaze aka the Fourth Hokage from Naruto. In fact, the whole deal with the Nine-tailed Fox has just recently been revealed as the struggle between him and Obito Uchiha, with Obito using Minato's love for his wife/partner Kushina (then-host of the Nine-tailed fox) and their newborn son Naruto (future host of the same Fox) for his advantage. And we already knowhow THAT ended...
Hizashi Hyuga deserves a mention here, as the mere realization that his son Neji is a member of the Branch Family sends him into a murderous rage (which is stopped before it can begin courtesy of Hiashi activating his curse seal - and doing so is the first step in causing Neji to spend at least nine years of his life afterward as the inversion of this trope!)
Also Hiashi for killing that Cloud ninja for attempting to kidnap Hinata.
Not even a freaking typhoon could stop Kenzan Takakura from getting medical attention for his ill daughter Himari. And he still had enough pluck to shield one of his sons, Kanba, from a falling lamp. And had his other son Shouma been there, he would've protect the kid too.
Kotetsu T. Kaburagi of Tiger & Bunny may have a strained relationship with his daughter, Kaede, due to his job as a superhero (which she isn't aware of) meaning that he has to spend a lot of time away from home, but he's not about to let anything harm his little girl. This is showcased when he lifts a collapsed tree to save Kaede from a collapsing shrine even when his powers run out, and later, when Maverick has a gun to Kaede's head, Kotetsu reveals himself to be Not Quite Dead and punches Maverick in the face.
Sai Nanohara from Jubei Chan is almost always a Bumbling Dad, but once he learns that his daughter Jiyu is the reincarnation and Soul Jar of Yagyu Jubei, he decides not to stay aside and does what he can to help her. In fact, his first Papa Wolf act was calling out Yagyu Jubei himself upon his treatment of Jiyu. To Jubei's very face. And in the Grand Finale of the first season, Sai also manages to give Jiyu/Jubei a Cooldown Hug to dispossess her from Jubei's influence, putting himself at great risk to do so.