Downfall is chock full of (relatively) nice, non-combative people. When they decide to get busy it tends to get ugly, mostly because the non-aggressive characters are usually the more powerful ones.
The Wizard in the Shadows has Harry, after he opens up a little. Nice, friendly, caring and slightly but harmlessly mad. Until you hurt someone he cares about. Then you are reminded that he earned his status as The Dreaded for the forces of evil, and that he is the most powerful mortal wizard alive. When Harry gets angry, craters the size of soccer pitches are left behind and the Nazgul make for the hills.
Child Of The Storm(by the same author as the above, who seems to like this trope) has, again, Harry. This version is warm hearted, friendly and is entirely without prejudice. It doesn't matter if you're a ten foot tall Frost Giant or flamboyantly gay French speedster, he'll happily befriend you without caring what other people think. But heaven help you if you threaten someone he cares about, as he will show you that he is the son of Thor (then incarnated as James) and Lily Potter, a scion of the House of Odin, a consummate survivor, and he has the temper to go with it.
Also, he's the nephew of Loki. He gets creative.
Stray contains an incident where this trope is applied to Otacon, of all people. It turns out that the quirky, tenderhearted, non-action anime geek can be dangerously resourceful when backed into a corner.
Latias from Latias' Journey. She's depicted mostly as a gentle, somewhat timid and fearful Pokemon. That changes big time in Chapter 5. After watching a bunch of evil bird Pokemon butcher a bunch of baby Flying and Bug types in Wing Fortress, she goes completely apeshit. The end result: a bunch of enemy Flying types lying in pieces in nursery, followed by a Psychic attack so powerful that it could best be described as a psychic nuke. That is followed up with an even more obscenely powerful Fire (or Dragon) attack that completely obliterates Wing Fortress and a large piece of the surrounding forest. It is utterly terrifying but at the same time fuckingawesome.
In the Yu-Gi-Oh! GX Spirit Caller fan fiction, the protagonist Kaigen Kou is usually calm and slow to anger, but bullying or mistreating his friends releases a terribly ruthless and somewhat psychotic side. It's a bad idea to bully his friends, but sully the reputation of the woman he loves and you'll find yourself beaten half to death and inches away from being LIT ON FIRE.
In Fill the Moon, when Demyx happens to witness Xigbar being slightly wounded by Captain Barbossa, that minor injury towards his lover is enough to get him to snap, summoning a hurricane and capsizing the Black Pearl, along with drowning around one hundred Heartless and keeping the entire pirate crew at bay with the power of his magic. Don't piss off Demmy-kins.
Another nice, cute, sweet messiah you don't piss off? The little girl called Senayax. Once you lay a finger on her family or her pet Heartless, you are in for an absolute world of hurt. Hollowmoon, the Eldritch Abomination that lives inside her, and Kingdom Hearts itself? They found that fact out the hard way.
Granted, Eija Satomi from Divine Blood isn't adverse to dealing lethal force when necessary, but she is still extremely friendly, patient, kind and generally feels remorse when she is forced to kill. However, after the ghost of her second, divinemother killed the first blood-related adult other than her own mother, apparently out of no reason than spite, Eija's response was violent enough to catch the attention of an ongoing psychic battle between the soul(s) of a Humanoid Abomination and several Gods and Demons. The Humanoid Abomination ran away while almost everybody else watched Eija seal the ghost by drowning it in psychic representations of blood.
Later,Kasumi kills a banquet hall full of rebel gods using what appears to be blood magic-based poison, given that it was triggered by stabbing her own hand, which caused them to sudddenly keel over one by one.
Uriel in Manchester Lost. One moment he is falling off the edge of heaven (which Raphael notes has no edges) and forgetting how to fly, as well as being a general Cloud Cuckoolander the next he is throwing the 3rd most powerful demon in hell through several buildings and the remains are sizzling and in bits. Then, after a long battle, he nearly succeeds in ripping Lucifer in half, and throws him all over the place.
The dwarven noble protagonist in Dragon Age The Crown Of Thorns expected Faren, the DC, to hate him when he revealed to him that he always knew Rica was Bhelen's concubine and had never said anything. Faren doesn't really end up hating him but, since he hates Bhelen's guts (among other, deeper reasons), he still delivers a No-Holds-Barred Beatdown to the prince, leaving him with a broken jaw and a couple of snapped ribs for good measure, plus a swollen eye. At least Faren ends up regretting it, after getting a What the Hell, Hero? speech from Kallian Tabirs, the city elf warden and his love interest, plus finding out just why the guy withheld that from him. He only really realizes just how badly he flipped out after remembering that the DN has a particular problem that prevents healing magic from working on him, so Wynne can't just snap her fingers and make the horrid pain go away.
In Reflections, Luna cares deeply for Celestia. She also won't let her sister run from her problems.
In Welcome To The Brothel, the protagonist takes time to write letters to his mother that showcase just how truly vulnerable and sensitive he really is. That doesn't stop him from being a highly effective warrior.
Nationverse actually loves this Trope. Hypertime elemental (and Cloud Cuckoo Lander) Shift is normally pretty laid back. When Shift's zombie grandfather almost killed him (during Shift and Miss Martian's first date date), Miss Martian morphed into her giant, scary white martian form and tore the zombie to little pieces. When the zombie grandpa got better moments later, Shift snapped and stranded him in a dead alternate Hypertime after beating him up at superspeed. He thought to himself (in his normal fragmented manner), after the blur of his own movements, "Tastes terrible. Zombies taste like old Slim Jims. Makes sense. Need mouthwash after this." The nice one bit off a chunk of his undead grandfather.
Another example is Fauna's "freak out" stage. Fauna is a sweet natured, Technical PacifistGranola Girl with abilities (she'll never call them powers) close to Beast Boy's. Push her to the point where her shapeshifting snaps her brain, and she will come at you with everything, including cobra venom.
The Doctor: Do that and you will end your days screaming in the deep places of my mind.
Big Bad: Y-you wouldn't do that! You can't!
The Doctor: Why not? You would.
Big Bad: B-but you're the Doctor!
The Doctor: Ah, yes, that argument. Heard that one before. And you know me so well, do you? You called me a monster not long ago. But now–ah, now you plead for the Doctor, the compassionate, merciful, pacifist Doctor.
Matthew Streika. Definitely one of the nicest, most decent people in a book full of things trying their very hardest to kill almost everything else, and is trying his best to make sure said dangerous things stay well away from his home town. All he really wants is to make sure innocents don't get involved, and protect his friends. He does not go looking for trouble. That said, do not mess with Matthew. Because when you manage to get him into a fighting situation, he is utterly ruthless and ferocious in a fight, not even minding his own pain until all hostile forces are either running with their tails between their legs or dead.
Uzumaki Naruto in White Rain is usually a happy, friendly, and goofy Hokage. When he stops being happy, friendly, and goofy, property values in Kusagakure drop in a hurry.
Driad in Clash of the Elements. The outer guardian of the Frozen Palace learned this the hard way when Driad regained his memories of his life as an outer guardian and briefly returned to that form to combat him.
Dr. Watson in Mortality (along with every other relevant Sherlockian work by the author). Ordinarily, he's the nicest guy you'll ever meet. But you mess withSherlock Holmes, and may the Lord have mercy on your soul, because John H. Watson will not. In one chapter, he's captured a criminal to interrogate, and he plays the Deadly Doctor trope disturbingly straight and delivers a pretty scary Badass Boast:
“If your master’s actions destroy him whom I regard as — as the best and wisest man I have ever known… make no mistake that I shall hunt down, to a man, everyone who played a part in his destruction.”
MLP:FiM fanfics tend to be full of those.
In My Little Denarians Rarity is a proper lady and sickened at the idea of violence. But when her friends are in mortal danger, she is the first of the group to start using human-made firearms. There is also Twilight Sparkle, who doesn't want to kill anyone but at her power remains extremely dangerous (At one point, when one of her friends is injured, she flips out with a banishment spell, sending several dozen cultists to the Moon... unaware that Earth's moon has no atmosphere). Last but not least Cheerlee, who goes Mama Bear on an enemy stupid enough to take one of her students hostage.
The adult fic Xenophilia gives us Lyra Heartstrings. She is calm, friendly and reasonable, with a lot of sense of humor and a bit of snark. She is also a grand master of the Still Way, a unicorn telekinesis-based martial art, with enough control to Neck Snap you from across the street, without moving a muscle.
This is how Princess Luna is depicted in Progress. She is a kind-hearted alicorn, if socially awkward, but not many of the characters who get on her bad side remember the alicorn part until it's too late. Especially if her glasses are broken, as Angel has learnt.
Fluttershy in the Pony POV Series, as can be expected. Taken to logical conclusion when she snaps completely, getting corrupted in the same way as Princess Luna was and turning into the second Big Bad, Princess Gaia/Nightmare Whisper.
Later (or earlier, as it may be), during the Gaiden: Seven Dreams/Nightmares side story, Patch Took a Level in Badass, but still remains the goodhearted clown she's always been. However, her search for the fragments of the Rainbow Of Light leads her to the Pegasus Despot using the Blue Shard of Laughter to brainwash ponies and powering a city to become an Evil Overlord. He brainwashes her with it and makes her part of his brainwashed harem of mares, raping her repeatedly along with them. When she finally breaks free, she steals his fragment, shoots him in the leg, and leaves him to his Karmic Deathat the hooves of his now equally pissed off and unbrainwashed harem. She goes back to being herself afterwards, but it shows she's not someone to push too far.
Dark World!Derpy is another example. She's still a kindhearted Ditz and probably one of the nicest mares you could meet, but she's the new Element of Loyalty and has spent the last thousand years walking nonstop around Discord's castle, making her very strong without using her new Super Mode. She proceeds to help the rest of the Mane Cast defeat the blackbirds that have spent the last thousand years trying to eat her daughter (who was turned into a muffin) and send them to Ponythulu's realm to be eaten. Later on, the Valeyard makes the mistake of spending the entire fight with him tap dancing on her Berserk Buttons. The result? She crosses the Rage Breaking Point and beats him to death after his Regeneration Template has been destroyed, ignoring his pleads for mercy.
Princess Cadence is another example. She's the same nice, lovable person we saw in canon, but the two times she's been ticked off she ended up dishing out a Curbstomp Battle to cosmic horrors. And when she becomes Queen of the Changelings at the end of the Wedding Arc, she sentences Kabuto, Chrysalis' unrepenting sociopathic Mad Scientist, to several centuries (at minimum) sealed insidethe sun, and completely aware.
In the Mass Effect The Equestrian Equation series, this is a racial trait of Equestrians and their ancient ancestors, the Equines. They are, and were, friendly, cooperative, and believers in the Last-Second Chance. That said, they would and do deal swiftly and with overwhelming force against those who refuse to play nice.
It's further backed up by biological instinct; amongst Equestrians, conflict typically takes the form of getting up in each other's face, then a staring contest, and only then in violence if neither backs down. Other races don't get that level of generosity; if they don't back down when the Equestrian starts getting aggressive back, then the Equestrian will attack. Dr. Milligan finds this out the hard way and is crushed to death by Twilight Sparkle's biotic powers, then thrown into the heart of an artificial star, for attacking Shephard and trying to commit genocide on the Equestrians in hopes of claiming the technological lore of their ancestors.
The Codex describes how the first and only major war the Equines had with another race went down. To put it simply, they annihilated their enemy militarily, economically, and politically, leaving not a trace behind.
Cadence in The God Squad. She has 1) Made to stallions impregnate each other 2) wiped out a mob of rapists 3) Threatened to sterilize every zebra and thus render the species extinct (after they threaten Shining).
Raspberry Beryl in A Hairier Problem Rise Of The Furball. She is usually rather meek, shy, and averse to talking with ponies due to her Dark and Troubled Past, but if you threaten to kill (or possess) an innocent pony or threaten (or Celestia help you, HARM) her pet phoenix she WILL try to rip the perpetrator to shreds with her dark magic. Prince Blueblood finds this out the hard way when he attempts to sabotage her trial by stealing Heliodor and causing the phoenix's emotional trauma to reach a point that his reincarnation cycle is shuffled up one year early. The guards barely reach him in time to allow him and Beryl one last tearful goodbye before he goes up in a burst of flame. In a rage Beryl completely freezes everyone in the room, verbally unloads on a scared shitless Blueblood, traps all of him but his snout in dark crystal, and is only saved from actually killing him with Apple Bloom's timely arrival and Cooldown Hug.
Uplifted, a Mass Effect fic set in the middle of World War 2 features a young Wehrmacht NCO named Heinrich Fuhrmann. Heinrich is a soft spoken, gentle giant, who frequently stammers, refuses to shoot wounded soldiers or the men trying to save them and frequently finds himself duped by his superior officer, Joachim Hoch. However, whatever you do, don't try to shoot him. You might find yourself getting a bayonet in your chest or hit by enough molotov cocktails and machine gun fire to kill a small army.
Jago from Ah Archfall. Nice guy. But at the bare minimum of his power, he flattened three bikers WHILE DRUNK. And if he uses Jupiter...
In There's Nothing Like a Fresh Pair of Eyes, student Assassin Catherine Perry-Bowen gets conclusively even with school bully Lucinda Rust after years of humiliation in the sword-fighting class. It helps that her vision and ability to fight have been enhanced somewhat...
In the Hunger Games fanfic Some Semblance of Meaning, heroine Vale Whitaker is probably one of the most sweet-natured, timid tributes in the Games. She hates the idea of harming another human being. This same girl lividly stabs another girl in the chest after the latter attacks Vale's district partner Kit, and after one of the Gamemakers' mutts kills Kit, Vale goes into what could be described as a berserker rage the next time she sees the mutt, jumping on it and hacking at it until it's dead and she passes out. To say nothing of the distrustful snark she unleashes on Obsidian Citrine, even if he's being perfectly friendly to her.
The inhabitants of Equestria have declared their universe a sanctuary for all those caught up in The Infinite Loops. That means they will not tolerate anything severely dangerous or morally wrong, and they have banished visitors to the moon for breaking the rules.
Sai in the Naruto fanfic Kitsune no Ken: Fist of the Fox is a polite, pleasant high school student who spends his time drawing and painting portraits, including painting his fellow students on his canvas if they ask him. But when four bullies destroy one of his paintings to intimidate him...let's just say Kakashi had to intervene quickly to stop Sai from killing one of them, AFTER he'd already beaten the four of them to within an inch of their lives.
"I never wanted your power just as much as you never wanted to be within my fucking belly! Our fates sadly have seemingly intertwined, for what purpose can only be known for the future, however, I will not tolerate your behaviour as long as I am like this! I will not be told of my faults and my mistakes! I will not be told I am weak by the creature who himself is weak because he does not understand the meaning of compassion! So as long as you are in my fucking insides, I will expect you to shut up and curl in the fucking corner of your cage, do I make myself clear?!" The young Namikaze said coldly before he turned a full angle and walked away from the cage, leaving a silent, shocked, and aggravated fox.
However the blonde paused as his fingers twitched with lightning and he turned and shot a large fully charged bolt of lightning at the fox's face, hitting him directly in his right side and striking a heavy blow on the beast's eye. This had cause Kurama to flinch back and growl in slight anguish as it covered his right eye in anger.
"One more thing..." The temperature dropped around Naruto as he gazed back "I do not care if you hate me or want me dead, I don't care at this point, however let me give you one final warning..." His eye glowed a cold azure blue as he stared at the Kyuubi no Yoko. "I don't care if you are a god or a tailed beast, or even the first Hokage himself...you will not talk bad about my father and think that your word will not go unpunished. I will make your life a living hell if you want to boast and degrade the works of the dead and the sacrifices that they had to make in order to keep their world safe just a little more."
Koushiro "Izzy" Izumi is one of the 3 nicest boys in the Digidestineds. In The Truth by Cybra, he discovers that his biological parents were murdered, is nearly drowned and finally nearly killed by his parents' murderer in a replica of their "accident". How does our sweet little computer genius react? By swiping the guy's gun and holding him at point-blank range until he gets the full story out of the guy. This not only scares the doctor he's threatening but also the watching Matt. The best part? The gun didn't have any bullets left and when Izzy is asked why he held the man at gun point if he knew he couldn't shoot him, he replies "I wanted him to know how it feels to be toyed with." Moral: Do not mess with Izzy or the people he cares about.
Lu Ten: Now you listen to me, Uncle, and listen good. If you hurt either one of those kids again, if you say anything to make them feel bad, if you so much as look at them wrong, I will face you in an Agni Kai and I will break and humiliate you in front of the whole court. I don't care who you are. I don't care if our family is watching. I'll hold nothing back, I will destroy you!
In Chrono Cross fanfic Fellowship, Guile is a kind and soft-spoken Black Mage who treats his little friends like his children and sometimes sheds Tender Tears. However, if you hurt or threaten any of his 'children', he will snap and proceed to pulverize you.