Durarara!! Mikado Ryugamine is a great example of this trope. He may seem quiet and nice, but underneath he's quite unstable. He's the leader of the Dollars, for another. You do not want to tick him off.
Machinedramon from Digimon Adventure is a villainous version. Don't let his whispered monotone fool you; he's as powerful and sadistic as any of the other Dark Masters.
Tetsuya Kuroko from Kuroko no Basuke is a good example as well. Practically invisible, he doesn't really talk much and people don't notice him. But if you try to dirty the game of basketball through nasty tricks...
Bertolt Hoover from Attack on Titan is a soft-spoken Extreme Doormat with absolutely dismal self-confidence. He spends much of his time lingering around the others awkwardly, and rarely offers more than a few words. He's also a highly skilled soldier, graduating 3rd in his class, and fiercely protective of the people he cares about. He also happens to be the Secret Identity of the Colossal Titan, and as such a Person of Mass Destruction responsible for wiping out 20% of the human race. While remorseful over it, he's fully prepared to do whatever is necessary to accomplish his mission. Beware the quiet ones, indeed.
Ai Emma, the titular Hell Girl is the most reserved character in the series as her job requires her to supress her emotions to the point where it is very difficult to make her angry... God help you if you actually succeed.
Shiryu from Saint Seiya is a softspoken Genius Bruiser with lots of common sense and a great devotion to his Master, his Childhood Friend, his Goddess of liege and his True Companions. He also represents the Dragon constellation and wears the Dragon Cloth... and according to Shiryu himself, the Dragon is calm and wise until those he cares for are threatened/hurt/killed/etc. in any way. Guess what happens to Shiryu whenever this happens? And even more so if either his Master or Childhood Friend are the one in danger...
"It's the quiet ones you've got to watch." You know that one, eh? Every time you see a story about a Serial Killer on TV, what do they do? They bring on the neighbor. And the neighbor says, "Well, he was always very quiet." And someone in the room says, "It's the quiet ones you've got to watch." This sounds to me like a very dangerous assumption. I'll bet you anything that while you're watching a quiet one, a noisy one will fucking kill you! Suppose you're in a bar and one guy's sitting over the side, reading a book, not bothering anybody, and another guy is standing on the front with a machete, banging on the bar, screaming, "I'll kill the next motherfucker who comes in here!" Who are you going to watch? You're goddamn right.
Fans of Blink may not know that she was introduced on Earth-616 during the Phalanx Covenant as a very shy, introverted girl named Clarice Ferguson who was terrified of her own powers. When she finally cut loose, she killed the formerly unstoppable Phalanx unit that had been holding her and a group of other young mutants captive... at the cost of her own life. The Blink who joined the Exiles was from an alternate timeline.
Monet St. Croix was introduced in the same storyline, and also fit the trope. She spent most of her first issue silently studying Phalanx technology until she could identify the impostor hiding among her fellow mutant prisoners. Then she hit him with a Megaton Punch and led a breakout. Even cooler than it sounds — she appeared to be catatonic at first. Turns out this was just a super-intense state of concentration, and she'd worked everything out... look out, Phalanx.
Batgirl 2000: Cassandra Cain was originally mute, and after learning speech she doesn't talk much. That's because her dad taught her to talk with her fists. Heaven help you if you get her mad.
Spider-Man: The Spot used to be a Spider-Man villain known for being largely ineffectual and mouthing off. Then he got trapped in the dimension he teleports through. Now he's mute, insane... and probably one of the deadliest killers alive.
The Inhumans: Black Bolt. Whenever he utters a sound, it destroys things on a major scale. That is to say, a whisper from him is on the level of a nuke.
X-23 rarely spoke at all in her first appearance (NYX) and origin story, (Innocence Lost) and even after is a laconic girl who generally shuns the company of others. She's also a highly-trained assassin and one of the most dangerous killers in the main Marvel Universe. God help you if you harm one of the handful of people she actually cares about.
In Ghostbusters, Walter Peck shuts down the power to the Firehouse despite Egon's dire warnings that it would be like dropping a bomb on the city. This results in an enormous explosion and hundreds (possibly thousands) of ghosts being released back into New York all at once. Peck orders some nearby police to arrest the Ghostbusters, claiming they were directly responsible for causing the explosion. Egon completely loses it, screams "YOUR MOTHER!!" and has to be physically restrained from tearing Peck apart with his bare hands. Remember, this is Egon Spengler!
Office Space: Beware Milton. Or he'll set the building on fire.
Thor's antagonist, Loki, started as the often pushed-aside, quiet, intelligent younger brother who was given too much power at exactly the wrong time.
In The Outsiders, Johnny was the most quiet and most law-abiding of the greasers but when he sees his friend Ponyboy being drowned, he stabbed and killed the attacker.
Harry Potter: Quirinus Quirrell is the nervous, mostly unnoticed and seemingly innocent character throughout the entire novel. However, at the end it turns out that he has been possessed by Voldemort all along and has been trying to kill Harry all through the book. However, he was probably being controlled by Voldemort by this time as he had been taken over after trying to seek him out to destroy him in his weakened state, trying to earn some respect from his friends and fellow school pupils that had laughed at him for so long.
Dark Life has Pretty. Despite his name, he is not someone you want to annoy.
Steapa from Bernard Cornwell's The Saxon Stories. Quiet and originally believed by the protagonist to be a half-wit, he becomes an absolute killing machine in battle.
Ben from The Leonard Regime is much more reserved than most of the other characters, bur provoking him is never a good idea.
Roose Bolton from A Song of Ice and Fire is a mid-level lord, and bannerman to the Starks of Winterfell (the "good guys" of the series). His obsessive habit of leeching himself leaves his voice very weak and whispery, so that everyone has to lean in to hear him speak during strategy conferences, and he loses the first battle he's sent to command in. Later, he betrays and personally murders his liege, King Robb, and is declared the new Lord Paramount of the North. It turns out he was working for Tywin Lannister all along, and kept over half of Robb's troops sitting on their asses for the war, later sending most of them to die in a pointless fight. Even the Lannisters underestimate him, as it turns out that after Tywin Lannister's death and the complete anarchy that falls upon the kingdoms, Bolton may be considering declaring himself the new King in the North and seceding, since the southeners wouldn't be able to do much about it anymore. Of course, the House Symbol should have been a hint.
Theodore Sturgeon 's short SF story "Extrapolation" was originally published under the title "Beware The Fury", as in the phrase "Beware the fury of a patient man". Wolf Reger is a brilliant but aloof and antisocial scientist/astronaut and humanity's future depends on his actions. When he is captured by alien invaders , Earth's governments all think he has turned traitor. But he manages to destroy the alien fleet single-handled without even using a weapon.
Beka Cooper, the protagonist of Provost's Dog. While she's paralyzingly shy, she's very good at chasing down criminals and fighting. (She does become less shy, but rarely chatty.) She has also been known to blow up at people who have been frustrating her over a long period of time.
Person of Interest: Reese tends to whisper when he talks. He prefers to let his actions speak for him.
Breaking Bad: the Cousins, a pair of assassins working for the Cartel, barely say a word in all the time they appear in the series.
Ronnie Gardocki was by far the least noticeable or interesting member of The Shield's Strike Team originally, but by the final seasons it was shown that his quiet demeanor hid a ruthless, ice-cold professional.
Saito Hajime in Hakuōki is the quietest member of the Shinsengumi and the one who can always be depended on to follow orders scrupulously and faithfully. He's also the most lethal swordsman of the group and practices iaijutsu specifically because it allows him to end most of his fights before his opponents know they've started.
Played for Laughs with Mio from Little Busters!. On the surface she seems like a delicate, fragile Emotionless Girl. And indeed, her physical stats are quite low. But she's very intelligent and downright ruthless at times, such as when she takes advantage of every slight lapse in attention on Haruka's part during the newspaper fight and is able to hit her countless times, or when she performs an absolutely devastating take-down of Haruka's joke when they're only supposed to be performing a simple Boke and Tsukkomi Routine.
Kiryuu Moeka in Steins;Gate is a very socially withdrawn woman and prefers to let her text messages communicate for her instead of talking. Even when the person she's texting is literally standing right in front of her. Take a guess at whathappens when you steal her phone.
Yuki Sonada kind of fits this trope (more since her magical girl abilities awakened, than in her earlier appearances). That is, assuming she's not just being stereotyped as an over-emotional teenage girl.
Precocious: It took a while, but Yvette has finally found someone to be nemesis to.
On Strip Search, Katie Rice is absolutely the quietest person in the house, but it soon becomes clear that she's also one of the best competitors — starting when she wins two elimination challenges in a row.
The Noob franchise has Ivy, narcoleptic and apparently not much more aware of what is going on when awake. But just try attacking one of her guildmates while turning your back to her...
Flora from Winx Club is sometimes thought to be a pushover because of her shy nature, hesitance to harm living things, and the nature of her powers. But time and again, she proves that nature is not so harmless, especially in Tears from the Black Willow, when the Trix hit her Berserk Button.
Fluttershy is the quietest member of the mane cast, on account of being, well, shy. Then comes "The Best Night Ever". When she's avoided by the forest creatures of Canterlot... well,see for yourself. Fluttershy in "Putting Your Hoof Down." Dear Celestia.... She displayed this way earlier, in "Dragonshy" and again in "Stare Master". "Dragonshy" is the episode where the fans learned that you do not mess with Fluttershy. From Season Four, "Power Ponies" demonstrates that you wouldn't like Fluttershy when she's angry.
Also, Celestia help you if Big Macintosh raises his voice.
The Transformers Prime version of Soundwave speaks using others' recorded sentences (when he speaks at all), rarely ever has a major starring role... and can bash in heads with the greatest of ease, as Airachnidcan attest to. He's the second-most feared Decepticon on the Nemesis, right under Megatron himself, and with good reason. Knock Out even says "Watch out for the quiet ones" to Breakdown after Soundwave curbstomped Airachnid. Wheeljack fared slightly better against Soundwave than Airachnid did. But only slightly. To put this in more perspective, Wheeljack had an easier time against Dreadwing. Soundwave is eerily silent when he fights, too. It's kinda Creepy Awesome.
In Transformers Animated, Prowl definitely qualifies for this. He's a sleek, dark ninja who doesn't really like anyone else, prefers to sit in his tree and meditate.. but when he fights, he wins, most of the time.