Also in a Marvel vein, during Civil War (specifically Runaways and Young Avengers crossover) when the Young Avengers arrive to find the Runaways lair, they meet 11 year old Molly Hayes outside. Due to a mix-up, Molly assumes they are bad guys and "hides under their car". Now by "hide under their car" we mean find a better place to lift the car and throw it at them. Yeah, they were not really expecting that. Earlier in the Runaways' series, when Wolverine scared her at the front of a cathedral, the comic cuts from him starting to threaten her to shut her up... to him flying across the street outside.
In both the animated Sonic the Hedgehog and the Archie comic series, Bunnie Rabbot has brute strength coming from being a cyborg, although you probably won't see her killing anything more objectionable than a few (dozen) robots.
A more straight example is Thunderbolt the Chinchilla. Of all of Dr. Eggman's Egg Bosses, she's easily the smallest, being barely bigger than Chip. She's also capable of generating an impressive amount of electricity to shock her foes and is extremely vicious and foul-tempered to boot.
Nextwave features some "Unusual Weapons of Mass Destruction", including the Drop Bears — koala bears trained to kill, which are deployed by throwing them out of an aircraft. "Cuddly widdle bears of DEATH?!" This is based on a joke played by Australians on tourists. See the Real Life section for more.
Lockheed, the tiny sapient alien dragon that befriended Kitty Pryde of the X-Men. He's so adorable that most people tend to forget the "sapient" and "dragon" parts.
In his introduction, the Brood were running terrified from him as he burnt their nests. The X-Men assumed he was some terrible monster until they finally saw him...
There was a Doctor Who Magazine comic, "The Star Beast", where the villain was named "Beep the Meep", a wide-eyed alien ball of fluff who just happened to be an unrepentant omnicidal bloodthirsty intergalactic war criminal. Beep proved memorable enough that he got two followup strips and an audio drama.
In The DCU, there is a rival group to the Green Lantern Corps called The Red Lantern Corps, whose rings are powered by rage. One of the members of the Red Lanterns is a cute-looking kitty... and he is just as dangerous as any other member. Don't fall for Dex-Starr's "innocent" act....
Pinocchio Vampire Slayer: The Rabbits of Ill Portent. They don't actually kill but they are quite creepy.
Gold Digger: Tangent features the "Death Lepus", also known as Wabbits — relatively small, rabbit-like creatures that look pretty cute, but are intelligent, pack-hunting carnivores capable of bringing down fully-grown dragons. The cute is also negated somewhat by their prehensile tails all ending in deadly magically-enhanced bladed weapons. Worse, the pack Alpha has a lycanthrophic bite that can turn a living victim into a Wabbit, than it can dominate like a master vampire.
The Mouse Guard is a band of skilled warriors who are also, as the title indicates, mice. They've been seen taking down predators many times their size, from snakes to owls and even a bear, although that was only seen in Legends of the Guard.
Diabolik has Eva Kant. She looks like an harmless blonde woman... Who has been raised in an Orphanage of Fear until she burned off the face of the Alpha Bitch and literally stole her ticket to liberty, worked as an hypercompetent industrial spy, and insists that her husband's death devoured by a panther was an accident because they were trying to kill each other, and she didn't mean to set on him the panther he had set on her. And sometimes even her lover, Diabolik (who is known as King of Terror for good reasons), acts as if he is scared of her. Quite tellingly, her first encounter with Clerville's criminals (a couple days before she met Diabolik) involved her beating up a mugger who tried to steal her purse and calling him a cretin for not understanding he was that outmatched (she had tried to let him go without the purse, but he didn't know when to fold them...).
Oh, and the thing about her husband? He was her uncle, who had driven her mother to suicide and sent Eva to the Orphanage of Fear after taking her family name away, and, upon stumbling on him in South Africa, Eva only married him to get back the Kant name and exact an horrible revenge on him: remembering him his crimes by her very presence (it helps that she really resembles her mother), with him unable to do anything about that because she'd otherwise reveal to the word their relation, and cockblocking him forever to add insult to injury (she'd never have sex with him in spite of his obvious attraction for her, and would prevent him from having lovers or rape women). And caused him an almost fatal heart attack by telling him just that on their wedding night. And when she finally started thinking about killing him, it was because she was getting bored (her dear husband did his attempt that very night because he was just that desperate).
In an issue of Weird Fantasy, in a story entitled "The Enemies of the Colony," colonists from Earth settle on a distant planet where they discover two species of animal — the cute, monkeylike Moku and giant, hideous beats called Hydrafiles. Moku are kept and bred by the colonists as pets, and Hydrafiles are constantly threatening the colonists' safety. When the colony leader's son turns up dead and horribly mutilated, it is assumed to be the work of Hydrafiles, and the colony leader declares all-out war against them. After wiping out virtually the entire Hydrafile population, it is revealed that the super-cute Moku become vicious in numbers, and the Hydrafiles were only attempting to keep their population down. Disaster ensues for the colonists.
One issue of The Simpsons has Homer in a deadly game show being dropped into a room full of adorable little puppies. Apparently the trap wasn't working properly, since he was supposed to be dunked in barbecue sauce first. Mr. Burns (who is the man behind the game show) angrily defends the choice, claiming his grandmother was "eaten by a roving band of puppies during the lean years of the Hoover administration".
Yet another Marvel example in X-23, the teenaged Opposite-Sex Clone of Wolverine. Physically she's quite unimposing, generally being depicted as slight, pretty teenage girl. She's also one of the most deadly assassins in the entire Marvel Universe, having a body count into the hundreds, if not thousands. By the time she was thirteen. On numerous missions Laura has been shown actively taking advantage of this trope by playing up her harmless appearance (whether by disguising herself as a handicapped girl, or a Girl Scout selling cookies, etc.). Even experienced agents like Alisande Morales, who have been extensively briefed on her activities, are stunned when they actually see her for the first time.
After The Queen of Witches in Hellboy banishes her right-hand pig man Grugach for doubting her power, she picks the cute little hedgehog as her new champion and general for her crusade to destroy all of mankind. Once she coats him in the blood of the fairy queen Mab, he turns into a troll even bigger and stronger than Hellboy.
Mr. Glum in Savage Dragon looks like a small, cutsy red doll with a rather harmless name, but he is not to be underestimated, as he is a Galactic Conquerer that has laid waste to countless worlds in his dimension and threatened Earth on regular basis. He uses a Powered Armor to pull any of this off for most of the time though.