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.
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.
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.
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.
Spike: WHY WOULD YOU LEAVE ME WITH SOMEONE LIKE HER? Sonic: WHY DO YOU THINK I SAID DON'T MAKE HER ANGRY? WHAT, YOU THINK I WAS BEING CUTE?
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.