The normally-patient, soft-spoken, and all-around good ol' boy, The Engineer, a.k.a. Dell Conagher, from Team Fortress 2. While being physically-accosted by his employer who (by product of the Not-Dying Machine his grandfather built) is electrocuting him, calmly and insistently states the following:
Engineer: I appreciate that you're my employer, and an old man besides... but if you don't take your goddamn hands off me I will break you in half.
Really, a lot of the team are this, especially around children, but in the field they are mentally unbalanced, bloodthirsty lunatics. Taken to the logical extreme with the Pyro.
The Halo novels confirm this for Cortana. She's a nice, somewhat snarky, AI who will get you transferred onto the front line and ruin your marriage if you mess with her or John.
Sonic the Hedgehog: Cream the Rabbit, and her pet sidekick Cheese the Chao. She's amazingly polite, gentle, and nice to everyone. However, if you try to piss her off in anyway (particularly you, Dr. Eggman), she'll beat the living daylights out of you using her pet Chao. As if her Game Breaker status in her debut title wasn't enough of a clue.
Try to kill Sonic when Tails is around. Just try it. He'll end your ass if you do, as Eggman found the hard way in Sonic Adventure 2
Sonic himself is generally an easy-going free spirit with no real ill will towards anyone. Cross anyone he cares about, however, and he'll plow through armies at Mach 3 to neutralize you, and that's when he's not even angry. Provoke him enough, and, provided he has the Chaos Emeralds around, he'll go Super Mode on your ass. Super Sonic is a Game Breaker of epic proportions.
Janos Audron of Legacy of Kain. In Soul Reaver 2 he's a kind old mystic and the only person who's relatively straight with Raziel. In Defiance he's even more so, with a dash of woobieness when he starts to realize everything he's been enduring centuries of isolation for has been wrong... and then he's possessed by the Hylden and you get a peak at what a true badass he is.
The title character from Mega Man X. Having just watched Zero sacrifice himself against Vile, X regains all his health and proceeds to dispense an asswhooping on Vile and then Sigma.
Maybe because X wasn't really one of the titular "Nice Ones," just a Technical Pacifist, and has been beating up robot masters for quite a while before the scene you're referring to takes place.
The predecessor Rock, though. Rock would be happy to while away his days as a lab assistant. When someone tries to use robots to attack people, though, he becomes Mega Man. He will plow through their forces, take their weapons to become a walking arsenal, and dismantle everything that stands between him and the threat. Lest you think Humongous Mecha will faze him, fuggedaboutit.
Especially in some of the later games, the original Mega Man nearly blows Wily away for good.
X in the Maverick Hunter X movie Day of Sigma definitely counts. Since it's set before the game, X was nothing more than a hesitant, unsure Hunter who took down criminals. Zero even remarks on how kind and sensitive X is. Then X scars Sigma's face with his bare hands after being stabbed in the gut.
Also, from the same game mentioned right above this entry, just right after you defeat Sigma's dog, X and Sigma will converse, and, oh my gosh, X was so angry, so angry, him shouting at Sigma alone can get you to crouch in a corner out of fear. X: I'll finish this right here, right now. I will defeat you Sigma!
Justified due to the final fight against Vile and its result (see spoiler above) are moved to the 3rd Sigma stage, which means they just happened, and X is probably still emotionally wounded over it.
Let's not forget Iris from X4. Kill a girl's brother, and that sweet little British girl in a beret will come after you in a giant purple mecha suit.
A manga adaptation of X2 as X being so disgusted with the fallout of the first game's events that he put a seal on his arm cannon (he thought only his left arm could transform; that lack of knowledge had a hand in Zero's death). After his unit is killed by a traitorous subordinate, X finally undoes it and fireshisX-buster.
Patrick Sprigs from Mega Man Star Force generally acts mild mannered and sympathetic, yet secretly harbors hatred towards the parents who abandoned him, which violently manifests itself as his Split Personality Rey.
Which is justified by the nature of the thing in question, as well as the fact that most of the shady characters more-or-less worship Serenade, the cyber-side keeper of the Undernet server and implied to be Mamoru's Navi.
Hibiki Takane of The Last Blade series is usually a kind, meek individual, who fights reluctantly. However, if the player keeps killing her opponents, she'll gain new win quotes and win poses included, and eventually a new ending that show her to have become a deranged murderer.
Vivi of Final Fantasy IX is sweet, innocent, kind, and despite his species, looks massively adorable, so naturally he has powerful black magic up the ying-yang. Most notably during the battle with Black Waltz 3 where the little guy just went ballistic.
In Super Robot Wars Gaiden, Tytti Noorbuck is considered one of the more nicer, gentle-hearted pilot. Except at one occasion when she found out that Ricardo Silvera have attempted a prank on her 'little brother' Masaki. What happens next was her furiously choking Ricardo, while keeping a smiling face (good thing she's stopped early). Conversely, she completely drops the 'Nice one' persona when she faces her arch-enemy Lubikka Hakinnen, due to many reasons.
The Seraphim, and to a lesser extent, the Aeon Illuminate of Supreme Commander are more or less defined by this trope-they're normally devoted to nothing but peace, love, and hope. Force them into fighting, and they try to make the fight as short and painless as possible. In this case, "short and painless" involves genocide in the form of planetary-scale bombing runs, nuclear strikes, liberal usage of Humongous Mecha, and massive waves of land, air, and naval robots of increasing size and firepower.
Bastila is a relatively nice person most of the time, but she does happen to have enough Force power to change the course of any battle ever.
Several more are like this. Carth? Genuine Nice Guy. Pulls you out of an escape pod and nurses you back to health. Takes it upon himself to act as your voice of conscience. Mention Saul Karath and your will had better be made out.
Zaalbar? Painfully shy Gentle Giant and very honorable young Wookiee...who can still rip your arms out and beat you to death with them.
Mission? Very sweet-natured teenager, forgiving to the point where it can be a Fatal Flaw...and lived by herself in one of the worst Wretched Hives in the galaxy.
Revan. Even if redeemed and pursuing the Light Side path, it's remarkable how everyone seems to forget that Revan was the Dark Lord of the Sith and should not be underestimated. As shown by the storming of the Star Forge, even following the Light-Side will not stop Revan from mowing through an entire army and mopping the floor with their former Apprentice.
Safiya of Neverwinter Nights 2 is a very kind person most of the time. Until you threaten her mother or her golems.
The turians are generally pretty nice guys, are almost all unbelievably polite. They're heavily militarized, but strongly civic-minded, highly responsible, steadfastly loyal, place the greater good before the individual, and are quite willing to work with and protect other, weaker civilizations or species. And if you provoke them into war, they make damn sure you are never able or willing go to war with them again. Ever. They conquer everyone they fightnote Except for the humans, which has ever since been a major sore spot for them. But give you compensation afterward, just to make it perfectly clear how well this fits.
The Asari race are this in every way, shape, and form. They were the very first Council races, prefer peace and understanding above all else (The Asari Councillor in particular is less abrasive and more peaceful then the brash accusatory taurian or the constantly questioning Salarian). Asari matriarchs are considered THE most powerful individuals in the galaxy and asari biotics are considered the best of the best to such a point that a data file says they are nigh-unbeatable in one-on-one combat. Considering that after the first stage of their life-cycles they start seeking mates and then after that stage they start the stage of trying to find peaceful teaching positions (mind you this is the point where they're considered one of the most powerful individuals in the galaxy), as you find out first-hand during the first game, they can be terrifying.
Most of the Galaxy are quietly terrified of the human race for this very reason. From their perspective, humans are a Giant Space Flea from Nowhere that despite only having 7 years of Mass Effect technology under their belt, simply showed up one day and somehow managed to hold their own against the might of the Turian military for several months! Then after a ceasefire was quickly brokered by the Council, the humans simply declared the entire thing to be a good match and proceeded to enter the galactic community under a banner of peace!
Liara's level of niceness is over nine thousand, but her powers are such that she can telekinetically bench-press a Geth Colossus, and launch people practically into orbit by thinking at them hard. Even Wrex makes a point of noting how damn powerful she is.
Kaidan Alenko is a relaxed, dorky type with absolutely no weapon skills available. But he can fire people into the sun with his mind and cause biological enemies to have toxic-flavoured seizures. He even ends his Training from Hell by snapping his turian instructor's neck with a biotic kick whilst defending another poor schmuck.
Tali is seen as being very polite and kind to most of her fellow crew members. If she runs across someone who she sees as evil, though, she can be... surprisingly vindictive. And amusingly creative; her reaction to a racist volus is to say that she knows intellectually that he's not worth getting worked up about, but emotionally she still wants to reprogram his suit's sensors to register the stench of garbage, all the time.
Commander Shepard him/herself can be the kindest, gentlest, supreme Paragon in the game. But even when played this way, s/he still gets a good share of ruthlessness, from threatening one of his/her crew with a gun to telling off news reporters who question him/her. S/he is also known for plowing through armies of geth, mercenaries, or Collectors and killing and pissing offReapers. For most of the first game, going pure Paragon makes it seem like Shepard simply cannot be angered, remaining polite and decent even in increasingly bizarre situations. Then the Overlord DLC from Mass Effect 2 rolls around, and the Paragon interrupt involves pistol-whipping a guy. Who completely deserved it.
In Mass Effect 2, Joker himself notes that Jacob is "way too nice a guy for all the ways he knows how to kill people."
Mordin is a doctor and one of the most helpful of characters, and also one of the most ruthless party members who easily butchered a few mercenaries that attempted to attack his clinic. And hung their corpses out front as a warning to anyone else who would try,
One of Zaeed Massani's old war stories include being nearly strangled to death by a hanar, a jellyfish-like race whose racial hat is unceasing politeness and piety.
Kasumi is probably the most social and outwardly altruistic character in the second game, but if you piss her off she'll turn invisible and shoot you in the face or Parkour her way onto your ship.
Legion Is a "True Geth" Which means he does not mind organic life, he's actively polite, willing to answer what questions you have, still likes the Quarians despite the war, and will hold conversations with you about philosophy and such. Just be careful of whether or not your priorities endanger his race, he will blow your face off with a anti-material rifle, or hack his way through every bit of personal data you have.
The true Geth in general. Remember that during the Morning War, they were peaceful, subservient and just sat around contemplating the nature of their own existence. They only retaliated when the Quarian government began arresting and eventually killing pro-Geth protesters, although the nature of their retaliation was somewhat extreme. Oh, and if their help is secured in 3, they can potentially provide as many war assets as the Krogan.
The title character of Conkers Bad Fur Day was already having a bad day - as the title implies. All he wanted to do was to go home after a night of drinking, encountering Vampires, Zombies, bloodthirsty Dogfish, Cavemen, Dinosaurs, Robotic Haystacks, a horde of evil Tediz and a gigantic, opera-singing turd. And more. He's remained almost saintishly calm, up until the last level, where his girlfriend is brutally murdered by his boss, and her corpse thrown out into space by the xenomorph out of Alien, named Heinrich. He then proceeds to throw it into space, THRICE, before decapitating it with a katana, in one of the most satisfying ends to any boss fight ever.
In a quest for Hunters, you have to kill four demons. The demons are in an alternate form. All of them are passive, and when spoken to, will respond cheerfully and positively, unless you are a Hunter. Three out of these four demons will use Fool's Plight on you if you even do as much as strike them.
In Cataclysm, there is the Shaman Erunak Stonespeaker within Vashj'ir. Very polite, saves your life a couple times, and doesn't seem very condusive to combat. Indeed, he doesn't get any combat...until the end quest. Then, he utterly OBLITERATES each force of Naga, one force with a MASSIVE Chain Lightning, and one commander simply by SLAMMING ITS FACE WITH HIS AXE. Believe me. You do NOT want to mess with this guy.
Cairne Bloodhoof, former chieftan of the Tauren. Very calm and peaceful guy. Kicked the ass of Warchief Garrosh Hellscream until treachery saw the end of his life. His son, Baine Bloodhoof, is basically the same way.
If Kingdom Hearts has shown one thing, it's that it's probably not a good idea to hack off Mickey Mouse...
To say nothing of the series' main character Sora. A happy-go-lucky kid who to date has defeated one thousand enemies in one fight, defeated most of the Disney villains at least once, and once cut a skyscraper in half and threw the pieces back at his opponent. (To be fair, the laws of physics weren't exactly in play during that last part, but still.)
We also learn that Goofy is capable of killing a man.
With only his shield at that, his character profile from the first game states that he flatly refuses too carry a sword or any other weapon of war, despite being Guard-Captain of the Royal Court Army in Disney Kingdom.
Yuna of Final Fantasy X. More in the sequel, but still in the original. To point: Yuna is captured by the Al Bhed. Tidus, Lulu, and Kimahri try to rescue her. After beating a boss, Yuna walks out of the hold on the boat she was imprisoned in, completely unharmed, and a guard slumps to the ground.
Lulu: I hope you hurt them.
Yuna: (modestly) A little.
Yuna is mostly the type who rather stays back in a fight and lets Auron, Khimari and Wakka or the Aeons handle the physical fighting. Though she keeps to casting healing and protective spells, you later learn why everyone is practically falling on their knees before her, and Badass Longcoat Auron and Kuudere Lulu allow her to run the show entirely as she sees fit.
Don't forget the sheer amount of damage Yuna's Aeons can cause. A fully charged Overdrive with the later Aeons can defeat most bosses single-handedly.
Early on she also can dish out more damage then the resident Black Mage Lulu if taught offensive spells.
And if you decide to take her down an offensive path on the Sphere Grid, she becomes a Lightning Bruiser that combines the offensive might and skills of someone like Auron with her own healing and defense spells. Lord help you if she decides to learn some black magic.
In BioShock you see the aftereffects of an object lesson in just how dangerous Little Sisters' Nigh-Invulnerability can make them if they're pushed far enough — in the area where they're converted, trained, and harvested, you find a corpse nailed to a wall with about a half-dozen of their giant syringes.
Also seen in the ending, where a bunch of Little Sisters swarm over the weakened Fontaine and keep stabbing him until he falls.
Leliana from Dragon Age: Origins is a sweet, fluffy, girly girl who used to be a nun. She wants to show mercy to practically every sentient being you meet that isn't a soulless husk of pure rampaging evil, and the main character loses her approval every time s/he chooses an evil or selfish action. She's also a retired spy/assassin who's killed more people than she can even remember and can be leveled up into one of the single most devastating ranged attackers possible in the game.
Also, Sandal. A young and innocent Idiot Savant who can only say "Enchantment" in various inflectionsnote Or so it seemed until Dragon Age 2, which reveals that he can also say "Not" without his adoptive Father directing him, you stumble across him for the last time just before the fight with the Big Bad. He's alone, unarmed, covered in blood, and surrounded by heaps of Darkspawn corpses (including two Ogres). When asked what happened he of course responds with only a cheerful "Enchantment!"
Merrill in Dragon Age II is a sweet, innocent, Adorkable young woman with some trouble adjusting to human society and an awesome accent. She is also a powerful blood mage and has a strong mastery of various ways to zap people into a fine red mist.
Bethany as well. Sweet, cheerful, and well-liked by all the other party members (Varric nicknames her Sunshine), she is nevertheless quite capable of sucking in all enemies in a large area with magical vortex before engulfing them with ice and flames.
And Sandal deserves mention here as well, seeing as he takes out a roomful of Abominations and Demons, including a 'Pride Demon', right before the final battle, while still having the same CloudCuckooLander personality as before. Not to mention his creepy prophecy that comes out of nowhere...
Wu Zi Mu of Grand Theft Auto: San Andreas, or "Woozie" to his friends, is a laid-back, friendly, unassuming Chinese man who enjoys playing video games, racing cars, and golf. He's also the boss of the Mountain Cloud Boys, a Triad sect - and when he finds his men wiped out and the Vietnamese gang responsible for it nearby, he rushes into the fray with a machine pistol and guns down everyone he can find, all the while shouting things like "Your blood will flow like wine!" - all this despite the fact that he's blind.
In Fire Emblem: Shadow Dragon, one of the few recruitable party units to attack you unprovoked is Wendell, the bishop who looks like the freaking pope. His dying quote mentions he has "no love for war", but you may remember that he's one of the only recruitable units who attacks unprovoked. Others include Roger, a hapless conscript who couldn't care less about war but doesn't have anything else going for him, and Jake, a gleeful ladies' man. Compare these with Darros the ruthless pirate and Navarre the stoic hired sword, who both try to talk to Marth or Caeda as soon as possible.
Occurs again in Path Of Radiance and Radiant Dawn. Ilyana, a weak thunder mage will try and kill you if you don't recruit her first. Mia, a nice swordgirl, can easily become the most competent sword-fighter excluding Ike. In Radiant Dawn, the main character is Micaiah, a nice, quiet light mage who can sacrifice her hitpoints to heal others. She's also the closest thing the Goddess of Choas has for a human embodiment.
Played with in Fire Emblem: The Sacred Stones in regards to Cormag. His supports show that he's a really nice guy, but he's beyond enraged when he meets the heroes, because he thinks they killed his brother. Once he's recruited, Cormag returns to his Nice Guy original personality... but when he finds his brother's true killer, he breaks into an short but very scary speech about how he'll enjoy killing the culprit, borderline Evil Laugh included. And then, when it's said and done, he returns definitely to the gentle person he almost always is.
Any good-aligned character in Fable games. In the second outing, and with enough experience, they will not hesitate to kick enemies in the face before chopping their head off with an enormous meat cleaver, knock them off of a cliff, shoot them in the crotch, knock their silly little attack aside and bash their heads in for their troubles, and all manner of other cruel applications of death and dismemberment. Probably while on their way to rescue slaves, collect on a bounty, or just give money to the church.
With the exception of Blue in Pokémon Red and Blue, every single Pokémon League Champion is perfectly friendly to the player in the field, then they clash for the title and pull out their team of Pokémon 15-20 levels higher than your own, all pumped up with the strongest moves they can know.
In Pokémon Gold and Silver, Gym Leader Jasmine is first seen literally having abandoned her post to take care of a sick Pokémon at the Olivine Lighthouse. She is also incredibly shy. Some more gameplay later, you get to fight her...and one of her Pokémon is a Steelix.
Also in Generation I, Red was a quiet boy who exemplified how important it is to care for Pokémon. After spending three years in Mt. Silver? Strongest trainer of the entire series.
In Emerald, Steven Stone is the equivalent of Red. Steven is generally friendly toward you throughout the story and even teams up with you to battle Team Magma in the Mossdeep Space Center. Once you beat the Champion, though, you can find Steven in the deepest chamber of Meteor Falls and battle him. His team consists of Skarmory, Claydol, Cradily, Armaldo, Aggron, and Metagross, and they are even more powerful than in Ruby and Sapphire as the Champion. The Prima Official Game Guide even says this:
He's friendly to you, but don't expect that friendliness to translate to the battlefield. He's merciless, and if you want to win, you must be, too.
Many Pokémon themselves also fit, like the sweet and innocent Togepi, who grows up into Togekiss who has the second-highest Special Attack of any Normal-type Pokémon. For a point of comparison, a Hyper Beam used by Togekiss is just as powerful as a Hyper Beam used by Arceus. And the Pokédex describes it as a harbinger of peace and goodness!
Cubone. Fridge Logic aside, there's a story of one that had its mother killed by Team Rocket. It picked up her skull and one of her bones and swore revenge. It doesn't help that back in the generation it was introduced, its evolved form could increase its Attack stat while attacking so much it would overflow. Did I mention it's a small, lonely Pokémon hiding inside an oversized skull?
Don't forget Dragonite. It's one of the most peaceful Pokémon in existence, until you realize its strongest move is called Outrage. You better not piss it off.
Guildmaster Wigglytuff of Pokemon Mystery Dungeon Explorers of Time and Explorers of Darkness is a fluffy pink rabbit who just wants to be everyone's friend. However, at one point in the game, he gets attacked from behind by three criminals he'd trusted. The outcome? All three of them are beaten to a pulp. This is mentioned as happening before when his team partner got knocked out by some bandits.
James, the God of Earth in Sacrifice, is very down-to-earth, stressing pacifism or diplomacy for the first half of the game. Later, when it becomes obvious that warfare is the only option, he grants you a few useful tricks if you're his follower. Tricks like the power to make entire sections of the world fall into the abyss. If you wind up attacking his home in the Glebe, your introduction to this ability (Bore) will be when it eradicates most of the large army you start the level with. A double-edged sword as units lost this way take their precious souls with them, but it has its place.
Earthworm Jim brings us Peter Puppy. At first, he seems like a cute little puppy. But if you dare piss him off, he will turn monstrous and beat you up For Massive Damage.
And from the prequel we have not just an attack, but a character who plays this trope fairly straight: Sagi is an Adorably Precociouschild who is a major Momma's Boy and does pretty much everything to get money for her to run the orphanage back in his hometown. He even takes most of the villains' actions in stride and stays pretty upbeat and friendly while they're off wreaking havoc. Push him too far, however, and nothing will stop him.
Who's the killer in Heavy Rain? It's not the crazy junkyard worker and car thief, Mad Jack, it's not the crazy Rabid Cop Carter Blake, and it's not even the Psychopathic Manchild Gordi Krammer. It's frigging Scott Shelby.
The Liir from Sword of the Stars are mainly kind, understanding Actual Pacifists. Until you piss them off. We'd call in the survivors of the last race to piss off the Liir as witnesses to this, but none appear to be alive as the Liir wiped them off the face of the Galaxy (although they appear to be back come the sequel). In-game, the Liir start out extremely positively towards all races except the Zuul and are very easy to placate as long as you keep the peace with them — but if they first get annoyed enough at you to start a war, you'll never get them to back down again: They'll come at you until you or them are dead.
The majority of Lux-Pain cast. Once they're infected with SILENT, you better look out.
MikeHaggar, Mayor of Metro City. Kidnap his daughter, and fear his pro-wrestling skills.
Dead or Alive: Kasumi is a sweet, kindhearted soul, and a Martial Pacifist through and through who makes it clear she dislikes even the thought of hurting others, much less killing. If you push her far enough or harm her loved ones and friends, though, you will know pain. Just ask Raidou, who, in the past, raped her mother, crippled her big brother Hayate and is an affront to everything she believes in and lives for. Oh wait, you can't: Kasumi killed him.
Super Smash Brothers Brawl showed that should the normally chivalrous but calm Link or Mario mistake you for severely harming their beloved Zelda/Peach, you will either get a sword or fist plowed into your skull. Based on their track records, you're more likely to survive the sword.
Wendy in Rule of Rose. The sweetest girl you ever meet, but also a jealous Yandere. Also the protagonist Jennifer, herself. She may be meek and submissive and faint easily, but if you push her around long enough, she will push back with strength that terrifies the entire Aristocrat Club.
The title character of Klonoa. In the first game, he's a really nice, fun-loving Kid Hero. He even borders on Cloud Cuckoo Lander occasionally. Then his grandfather is killed.Joka did NOT survive the next level.
Wheatley from Portal 2. Normally he's a rather friendly yet dim-witted robot who tries to help you escape from the lab. That is, so long as you don't call him a "Moron". Do that, and all hell breaks loose.
Garlot, protagonist of Blaze Union, is gentle and empathetic to a fault, and even though he has a short temper, he generally cools down very fast. He has self-confidence problems and spends a lot of his downtime wishing that everyone would just get along. And he's no pushover normally. But when bandit-by-any-other-name Pandra decides to sack Garlot's hometown, he goes into a state of cold rage so terrifying that every enemy in his path basically shits themselves in terror. In addition to this, inflicting serious harm on the people closest to him is a really, really bad idea.◊
Civilization: An Ascended Glitch turns Gandhi from very pacifistic to very militaristic when he invents Democracy. The game's Technology Tree means he can invent nuclear weapons soon afterward. If Gandhi threatens you with nukes, listen to what he has to say.
In Civilization V, Gandhi is the easiest leader to befriend. However, if you get on his bad side (be a warmonger, attack him personally), he will nuke your civilization into so much radioactive dust. Someone poked around the data for the game, and found a 1-10 scale on how likely a leader is to use nukes. The most warlike leaders (Montezuma and Alexander the Great) ranked about 8. Gandhi has a special rating of 12.
The Psilons in Master of Orion are generally pacifistic and do not actively seek to conquer other empires. However, they have the best research abilities in the game, and will invariably be higher on the tech tree than you, which means they'll thrash you in a war.
Fallout: New Vegas has a few of these. On the Player's Team there is Veronica, a Brotherhood Scribe who wants them to play nice instead of raiding anyone with energy weapons but can also murder your face with a power fist, Arcade Gannon, a Follower of the Apocalypse doctor and researcher who wants everyone to be happy but is also a former member of the Enclave well trained in Energy Weaponry, and ED-E, an eyebot that just wants love and to find a home. Cass could also count, but she's an example of Good Is Not Nice.
There's also Christine Royce, a deeply philosophical Brotherhood of Steel Scribe who was Veronica's lover. When their former elder, Elijah broke them up, she joined the Knights and the Circle of Steel. When she heard about Elijah murdering people all over the wastes and abandoning the BOS at Helios One, she volunteered to hunt him down and assassinate him, becoming one of three people to explore the Big Empty and escape before assisting the Courier in killing Elijah and becoming treated as invulnerable as the security holograms to the Ghost People.
There's also Marcus and Mean Son of Bitch, two very friendly Super Mutants. Marcus, however, was a player companion in Fallout 2 and helped blow up the Enclave's Oil Rig and Mean S.O.B. defends Westside against the fiends so well that most of them stay away from Westside now.
Most of the low-level NCR troopers and Rangers can be seen as this. Most of them are nice gentle people, but they can kick your ass. Special note goes to Private O'Hanrahan, who doesn't want to kill people but in certain endings helps assisting his squad single handedly stop a Legion assault on NCR Ranger HQ at Camp Golf.
Similarly, Yes Man is an A.I. programmed to be helpful to whomever gives him orders and his default personality can be described as overly cheery. However, he's also the mastermind behind the plot to hijack Mr. House' plan to take over Vegas from both the NCR and Caesar's Legion. He's also the one who planned the attack on the Courier at Goodsprings. You can confront him about this, at which point he apologizes (not knowing who you are until you tell him).
As with Mass Effect, the player character, the Courier, can be one too, if you choose the "nice" paths. And then you can haul out your gatling laser and proceed to utterly destroy that group of raiders that thought you were easy pickings...
Avion from Shadow of the Colossus is generally considered the second most peaceful colossus in the game, by virtue of the fact that it will never attack Wander until provoked. Until Wander makes an attempt to harm it, Avion is content to sit on its perch and watch him swim around the lake... but the second Wander shoots an arrow at it, Avion will come swooping down to divebomb him. This attack is a one hit kill in Hard mode if Wander is not successful at dodging it, and is pretty damn scary otherwise.
Super Mario Bros.: Luigi is generally a pretty nice guy. If you threaten to harm Mario, he becomes an unstoppable force. To whit, in Mario & Luigi: Dream Team, when Mario looks to be in extreme danger in the Dream World, Dreamy Luigi grows giant and in one case, slams backwards a sentient volcano only with his hammer! Even more impressive, Dreamy Luigi is able to hold his own against Giant Giant Bowser. As in, Giant Bowser made even more giant to the point where Giant Luigi barely comes up to his knee. The last Giant Battle is activated not by fear but by sheer willpower as well.
Luigi: Nobody messes with my bro!
Don't mock his mustache either. This was was actually very plot important: It was part of the Batman Gambit in Dimentio's Xanatos Gambit to get Luigi brainwashed and take over the worlds. He succeeded in brainwashing Luigi, but after... well, Dimentio became the only villain in the game to get a Game Over.
Before that, in Paper Mario: The Thousand-Year Door: The Happy Lucky Lottery is run by a nice, happy, optimistic Bob-Omb named Lucky. You get a new chance to win in one real time day, determined by the Gamecube/Wii clock. Unlike other games where you can abuse the clock if it affects the game... Lucky will go berserk if you do so. Do it twice and you get a Game Over.
Noel Vermillion's hobbies include shopping via the internet and writing poems. She likes cute things, and dislikes bugs, especially ones with lots of legs. That said, if you mock her chest size or her intellect, Bolverk will perforate your skull. Then there's also the fact that she can transform into Mu-12, which is her Super Mode and is dubbed as Kusanagi, the sword that slays gods.
Makoto Nanaya is a silly, friendly, generally whimsical and energetic person, and also appears to be somewhat scatter-brained. However, she makes it clear to Tager, "If, for whatever reason. Noel Vermillion is harmed in any way, I will hunt down that person and make them pay... dearly." This is neither hyperbole nor limited to Noel - attack any of her friends and, unless you're one of them (hi, Carl), you are in for a world of pain. Let's not forget that her Astral Heat involves punching the opponent so hard it shatters the moon.
Dark Dawn introduces Sveta Czamaral, a shy, sweet, troubled girl from the kingdom of Morgal. Who can turn into a seven-foot-tall werewolf with an attack rating that makes most of the game's bosses blush.
In Diablo III, the Hand of the Prophet are a group of girls who served under a powerful Vizjerei lord prior to encountering the aforementioned Prophet. Eirena, one of them, is quite friendly throughout the nephalem's campaign, and yet she was thirteen at the time she and her sisters murdered their lord, his buddies, and the greater daemon the Vizjerei were summoning.
Tales of the Abyss: Fon Master Ion is polite and friendly to a fault (and is rather feminine looking), but he wields some of the most powerful fonic artes in existence. Not only that, he's also one of the most powerful people in the world politically, and knows how to use that power effectively when push comes to shove...like the time when he threatened to stop reading the Score (the giant prophecy that everyone relies on to determine what they should do, often on a daily basis) for an entire country if any of his companions are harmed.
And come Hyperdimension Neptunia Victory, Plutia blows them all out of the water. Normally lazy, friendly and scatterbrained with just the vaguest hint of a slight sadist streak, major villains are known to rethink a confrontation if it means she might transform. Why? Because Iris Heart won't kill you. MadamGoddess will make you beg for permission to die.
Plutia is the most extreme; though Peashy gets this too. Even before she was transformed into Yellow Heart she routinely beat the crap out of people and she's cute as a button.
In a similar vein to Dr Mordin Solus in Mass Effect, Dr Lokin in Star Wars: The Old Republic is a talkative, polite old man. One might mistake him for a bit of a dork even, but under the facade he's a ruthless man who survived this long because he knows the tricks of the trade, and mind you, his trade is Imperial Intelligence.
And then there's Lord Zash, the nicest and most polite sith you will ever meet. Khem Val notes that she "reeks of death."
Likewise, a Light-side Sith player character is regarded as an oddity by non-Sith, while your fellow Sith (especially once you start climbing the ranks at breakneck speed) regard you as far beyond dangerous because they don't know the true limits of your power behind your facade of kindness and humility.
Louis of Left 4 Dead is the most optimistic of the survivors and generally keeps a positive attitude (which drives Francis nuts). However in the Death Toll campaign when the Church Guy refuses to open the safe room for them, Louis threatens to beat the crap out of him with his gun.
Louis: "Mister, if one of us gets killed out here, I will shoot my way in there and beat you to death with my gun!
All the yordles (minus Veigar, who is megalomaniac; and Rumble, who is basically an egotisitcal mad scientist) from League of Legends can easily fall into this trope. More particularly true with Teemo, who spent most of his time in isolation through his scouting missions and he's slowly show signs of his mentality being cracked apart. Luckily, he's good friends with Tristana and has her in company.