From the fic Ah! Archfall: you can do what you like to Jago, but you insult or threaten Lind, their unborn child or either of his Archs, and the very least he'll do is beat you senseless. And if you force him to summon Papa Jupiter to do it, he WILL kill you.
Avengers fanfiction has a ton of examples where Hulk gets mighty protective over Clint/Hawkeye, but none more so than Big Green Guardian Angel. The biggest scene in the one-shot was when Clint, after accidentally exposing the scars on his torso, explains that he got them as a kid, causing Banner to Hulk out right then and there. As if that wasn't "aww" eliciting enough, Hulk stopped his rampage enough to trace Clint's scars, whimper a little, and proceed to destroy everything in sight as a result of his rage.
Hawkeye becomes this to a de-aged agent Coulson in this story.
Loki, of all people, becomes this to his adopted daughter in the fic Mischief, Lies, and Other Hazards of Parenting and its sequel, Thor's Days. In the first he practically bolts to the park where she's having her birthday party when he thinks its being attacked by Dr. Doom (it wasn't), and in the second he almost snaps her scout leader's neck when she's injured due to said scout leader's incompetence (Tony intervened that time). And then in one chapter, Natasha comes to him and makes a hint that Clint might go near the girl. Loki's response is scary.
Loki: I will, however, show no mercy to anyone, and by anyone I mean your dear Agent Barton, who chooses to strike at me through her.
Natasha: So if Clint takes Kara, you'll kill him?
Loki: Has my dear brother ever told you how he and I would sneak into the orchards of the goddess Idunn when we were children? Those apples, which I was so very good at stealing, grant whoever eats them a very long, very resilient life. If your little friend does anything to Kara, I will find a way into Asgard and strip Idunn's orchard bare. I'll cram them down his throat and save enough for you, so you can watch as I torture him for eternity. No matter how much either of you beg me to kill him, he'll live through every length of gut ripped through his flesh, every severed limb, and every drop of acid spilling into his eye. Now is my meaning clear?
"You took my little brother, tied him up, pumped him full of heroin, and left him to die in this shit hole. Now I ask you: do you think I have the slightest bit of remorse about cutting you open and letting your guts decorate the floor?"
Thor gets a Crowning Moment of Awesome (that doubles as Crowning Moment of Funny) when the Ministry of Magic tries to take Harry away from Tony: Thor breaks in and calmly warns the Wizengamot that voting for taking Harry away would cause Thor to tear down the building and break all bones in every member of the Ministry. Harry then gets him to amend it into only tearing down the building and breaking the bones of everyone who voted yes (the rest of the Ministry people are innocent, and the Aurors that would try and fail to stop him are merely doing their job). The Wizengamot promptly vote to leave Harry with Tony.
Harry shows tendencies towards this in The Wizard In The Shadows, with generally whatever has been stupid enough to push the Berserk Button of hurting his friends being fried or straight up vaporised and a very large crater being left behind.
Matt: I know you're Kira or whatever... this is me impressed. Doesn't change the fact that if you start any funny business with her, I'll shoot you through the fucking wall. I'm quicker than you and your little Diary of Death. OK?
Light: It was you, wasn't it? You fucking tried to kill him!
V: I'm sorry, Light.
Light: Not going to cut it, V. I thought that you didn't want to kill L.
V: I don't.
Light: If you touch him, I'll kill you. I'll kill all of you.
Light: I will also keep the Death Note where I can reach it whenever I need to, because I will need that power to protect you and our orphans. But... would you, and could you, perhaps, consider... combining Kira and L's powers?
L: What, as in, 'Quit killing, or I'll set Kira on you'?
AUDevil May Cry fic "Like Father, Like Son" has Dante exhibiting his demonically-protective side when he finds his son Nero injured courtesy of a police officer with temper problems, and when Nero is later threatened by members of the mafia. The second time Nero gets threatened by the son of a mafia head, a partial Devil Trigger sends the man leaving with tail between legs. And when Dante finds the demon Baul, who had all but put Nero near Death's door... Cue Unstoppable Rage and Roaring Rampage of Revenge with a dash of There Is No Kill Like Overkill.
In Harry's New Home, Snape will go to any lengths to protect his ward Harry, even if it included breaking rules or facing the Dark Lord and Dumbledore (if necessary) to do it. For that matter, Dumbledore does not like seeing any of his students harmed in any way, especially if it's Harry. His Berserk Button was pressed when he found out Umbridge used a Blood Quill on Harry and in the prequel, he gave a casual warning to Snape who earlier in a fit of rage slapped Harry. All in a cheerful tone and a benign smile.
"You do understand that if you ever, ever again strike a student in so brutal a fashion, you will not survive the night, correct?"
In the Lord of the Rings fanfic Ancient Prophecy fullfilled, one of the Valar (the gods without Capital G) slew the children of their Guardians. Understandably the Guardians in question weren't so thrilled. They battled the Fourteen Valar, destroyed the city they dwelled in and still inspire such fear that the Valar have to call upon the in that fanfic formerBig Bad to aid them!
In Lord of the Rings fanfics such as An Eye For An Eye or The Roots of Evil, it is a sure way to trigger Legolas's Berserk Button is by hurting Aragorn in any way, shape or form. It is the same with his older adopted brothers Elladan and Elrohir, who must have gotten it from their father Elrond. All four elves have no hesitation to resort to killing anyone who dared lay a hand on Aragorn. And those times when they found that Aragorn was tortured and near death ... well, to say it did not go well with those people is putting it lightly.
In the AU fic Knocked Up, Megamind saves a pregnant Roxanne from an extremist group intending to do their unborn child harm. And then, after the baby is born...
Megamind: If anyone harms even a single hair on my daughter's head, or has a clear intention to do her, or her mother, harm, they will be obliterated with whatever weapon I can get my hands on quickest.
It should be noted that Megamind is a former supervillain.
As shown in the 7 Dreams/Nightmares side stories, Sweetheart's husband Teddy was this. When some corporate thugs tried to harm their family in order to intimidate their friends out of activating the world changing spell, he put them all in the hospital. And after the disaster caused by said spell failing, he fought off a group of smirughs that attacked the family when they were seeking refuge.
Lord Tydal in The God Squad takes Papa Wolf to the extreme. Tydal tells his group about how he raised Celestia and Luna when they were babies, after their Mother (the creator of all things) dumped them on him. When Commander Hurricane and the pegasi army march up to Tydal's Keep, demanding the foals, Tydal tells Hurricane that two other armies (these being unicorns and earth ponies) beat him there. Tydal then reveals hundreds of severed heads then delivers this speech:
“Celestia and Luna are my sisters and under my protection. Three times Equestria has come to my door… the next time I see a flick of a pony’s tail my army will march upon your pathetic little country and I will raze it to the ground. Your stallions will be slaughtered, your mares used for our pleasure and your foals sold as slaves. I will burn your forests and salt the earth so nothing will grow again. I will burn the skies and cover the lands in darkness. I will personally come to your little Cloudsdale and I will rip it down from its high perch and crush it under my hooves. And only when this is all done will I finally come for you and your fellow rulers… and then your agony will begin. I will visit death upon you a thousand times and still not let my brother the Reaper claim your souls. That is only a taste of what I will do if you EVER THREATEN MY LITTLE SISTERS AGAIN! So… in a word Commander… run."
Tydal gets another one in The God Squad's sequel, "Equestria's Most Wanted". After giving up violence and becoming a pacifist, he is seconds away from achieving full enlightenment... only for Celestia to scream "DADDY!" when she is attacked. Tydal instantly breaks his vow and brutally murders her attacker, then warns an entire asylum that he is going to destroy them if they come near his girls again.
Orochimaru of all people is one in the Fanfic called A Father's Wrath. In this story he is Naruto's father instead of Minato. On the lighter side he cares deeply for his son and his actions including joining Akatsuki and forming the Sound Village is to protect him and has found a source of Redemption. But threatening Naruto is the fastest way for him to remind you that he wasn't called The Snake Sannin for nothing. Just ask Hidan.
Naruto in Win Some, Lose Some, a collection of one-shots. Naruto's warning when Kurenai, Hanabi, Ebisu, and Konohamaru find out about his (adoptive) daughter basically amounts to "If you tell anyone about my daughter, I'll kill you. If anyone tries to harm her, I'll kill them. If anyone kills her, I'll burn Konoha to the ground." Turned Up to Eleven because the Nanabi is sealed within her, meaning the Kyuubi is protecting her too.
Daiki from Destiny Is A Hazy Thing is this for Naruto. One scene has him tampering with Naruto's seal to allow him, Naruto and the Kyuubi to talk with his real parents. He promptly spends several minutes slowly brutalizing Minato's soul.
One Piece's Muzzled shows a moment where Zoro literally resorts to biting Marines (after having his swords taken away and his hands tied) who tried to separate him and the kidnapped Usopp and Nami to trap Luffy.
Even more awesome than it sounds given his fighting style. His bites break bones.
Silver, from Pokemon The Great Adventure. The man is mercilessly protective toward Ash in particular and doesn't think twice before jumping at Mewtwo's throat for petrifying him. As the Legendaries say: "It's safer to attack a baby Kangaskhan in his mother's pouch than a kid Siver took under his wings". Did we mention he is a very old Ancient and an Ice Aura Master?
While it was established in the prequel books that Pitch was a Papa Wolf, the story Guardian of Light takes it Up to Eleven. While he starts out as an evil version of this trope early on, it eventually gets to the stage where he jumps off a cliff just to save his daughter, Helen.
Bunny and North have their moments as well, towards Sophie and Jack respectively.
In another story by the same author, called Lullabies, the Bennett children are orphaned and the Guardians adopt them. Then, one night, Pitch pays a visit. Bunny, who is guarding them, immediately gets into a fighting stance.
Bunny: You take one step towards these little nippers, and I'll rip you apart where you stand.
Light of the Snow Red Village is an AU fanfic that answers the question, what if Kenshin and Tomoe had a child? After Tomoe is killed much later in the timeline due to treachery from his superiors, Kenshin takes to wandering with his daughter Hikari. Throughout the story Kenshin is fiercely protective of her well being and happiness, even going so far barring her from learning kenjutsu (he later allows it, after it's pointed out by another character that it's hypocritical of him while he carries a sword himself). Following some adventures they eventually end up in Tokyo at the Kamiya Dojo, where the manga timeline begins. Currently incomplete, but it's a great story nonetheless.
Sleepwalker is deeply torn by angst and loneliness over his being exiled from his home dimension of the Mindscape and trapped in Rick Sheridan's mind. He doesn't have any doubt at all about one thing, though. If you threaten Rick Sheridan or any of Sleepwalker's other close human friends, you are in for a world of hurt.
Kirk (empowered by Khan's blood) in That Was A Good Fight. When a shapeshifting alien vampire thing threatened his crew, and specifically, Spock, they had to clean what remained of the creature out of the floor tiles.
Khan is the most prominent. Like in the film, he is this to his crew, and is prepared to kill Dr. Korby in the most painful way possible upon discovering that the man killed all but five members of his crew. He later nearly does carry it out after his surrogate daughter, Lucille, is taken by the man. Said surrogate daughter is able to convince him not to.
Spock gets a moment towards the end of the story. Korby kidnaps a pregnant Uhura too, and when Spock sees Korby hit her, he attacks him in rage.
Spock: (through a forced mind-meld) You hurt my bondmate. You threatened my child.
McCoy also has a moment when trying to take back his daughter, Joanna, from his crazy ex-wife. "Once you took everything from me, including her...and hell, I'm not letting you take her again!"
Kirk to his crew, and Lucille. Note that in this story, he's empowered by augment blood.
There was no way for the overwhelming wrath of God to be made evident through mere behavior. The archangel was no longer responding to the demon's mocking himself for the light that surrounded his already blinding form had no place on the conceptualized wavelength of mortal comprehension; it was the response of an incensed Father to the torture and ridicule of one of his sons, it was the vengeful mark of the Lord Himself.
In Supernatural's Crossing the Line, John Winchester kills a human being for the first time because it was heavily implied said person had molested/sexually assaulted a ten-year-old Sam.
In the Team Fortress 2 fic Paternal, the RED Spy becomes this to the BLU Scout, protecting him from the Administrator's henchmen at all costs and even facing down the Administrator herself to keep him safe. Discussed by the BLU Engineer in Chapter 26 after Heavy and Pyro express wishes to kill the Administrator's Spy for sexually assaulting Scout:
Engineer: Sorry, boys, but I think Red's earned the right to kill that son-of-a-bitch. I don't know if any of you are fathers, but I know that if someone had hurt my daughter, I'd take him out back and shoot his brains out for even touching her. I'm sure Red wants to do the same thing to Bane for what that snake did to his son.
Exploited by the Administrator, who knows that the RED Spy has a doomsday device activation code that she gave him many years ago when they were dating and which, in turn, is actually on a pair of dog tags that the RED Spy gave to the BLU Scout when he was little. After BLU Scout shows his father the tags, her plan changes shape: capture Scout and use him as a bargaining tool in exchange for the tags, knowing that the RED Spy will stop at nothing to ensure his son's safety.
Optimus Prime and Ratchet in Things We Don't Tell Humans. Optimus is a fan of children, and Elita puts off telling him about how badly Quicksilver was treated because she knows he'll react badly (he does, and it's a little terrifying). Ratchet tries to pick a fight with a general who dismisses Prowl as just a numbers guy.
Ironhide is implied to be one (and seems to have adopted Sam and Carly). So is Tom Banachek, if the Autobots' dread of telling Tom and Dana about Faust's "capture" is anything to go by.