Bunnicula has a vampire-like rabbit that Chester assumes is a killer rabbit, but there's no evidence that he ever actually does any harm whatsoever besides draining vegetables. Another author reimagined Bunnicula as an Evil Overlordwhich is pretty charming.
Codex Alera: The young cubs of the Canim are described as looking like adorable little puppies with opposable thumbs. They can also tear someone's hand off with just their fangs at only five years old, and also do so with enough force to dislocate someone's shoulder.
Dark Lord of Derkholm: One of Derk's experiments resulted in a flock of carnivorous sheep. This was apparently an accident, but it comes in handy when his children need to keep an army of dangerous criminals in line.
Dragaera: Norska are omnivorous rabbits that eat dragons.
The Edge Chronicles: The Deepwoods are full of all manner of horrific animals and plants, but the effectively undisputed top of the foodchain are wig-wigs. These are small, orange fluffballs that also happen to be pack hunters that can and will kill anything they can reach, no matter how big or strong it is. Their only real weakness is their inability to climb.
Hometown: One of the Heart Eater's primary servants is a coydog puppy. It has no more physical strength than any other puppy, but then, considering that it can Force-Choke a full-grown German Shepherd, it doesn't really need physical strength.
Honor Harrington: Treecats are cute, fluffy, six-limbed felinoids who are great with children, wonderful, supportive companions for life who'll be with you through thick and thin... and will turn into fuzzy, flying buzz saws if they think you're a threat to their kittens or adopted humans. Treecats think that enemies come in only two states: those that have been properly dealt with, and those that are still alive.
The Hunger Games: There are carnivorous squirrels, poisonous butterflies, killer monkeys, and much much more.
InCryptid: On their own, an Aeslin mouse is almost as vulnerable as an ordinary mouse, though they do make and use weapons. In a group, they've been known to take down large snakes, venomous gila monsters, and even alligators.
Oryx and Crake: Wolvogs look like friendly dogs and, when they are not ruthlessly killing other creatures, they act like friendly dogs. They can go from friendly to homicidal, and back, quickly.
Percy Jackson and the Olympians: Polyphemus' island is home to a flock of carnivorous, hippopotamus-sized sheep that can devour a deer in less than a minute, leaving only a pile of bones. Percy describes them as "piranhas with wool".
The Plague Star features creatures called "hellkittens", which spit wads of powerfully acidic saliva.
Rainbows End: Mr. Rabbit qualifies as "the next bad thing" in the eyes of one character. The previous "bad thing" was a plague worse than bubonic, and the one before that was the nuclear destruction of Chicago. It's never made clear how much rabbit-nature he actually has.
Redwall: Woodland creatures like hares, mice, otters, squirrels, hedgehogs, and even moles are all quite capable of becoming fierce warriors and defeating any vermin that threaten them. (Although a badger isn't exactly in a Killer Rabbit scenario when what it's fighting is a rat.) Basically, it's a World of Funny Animals where the "Funny Animals" are Killer Rabbits. Except the actual rabbits, ironically enough.
The Reefs of Space: The Planner's daughter, Donna Creery, is attended by a set of "peace doves"—beautiful birds which have been enhanced and trained to serve as deadly bodyguards.
Sixth of the Dusk: The island Patji is home to, among other deadly animals, mice with a single venomous tooth which, of course, can kill you. Unusually enough, they've actually been tamed and are one of the few things on the island not especially dangerous.
Ghost-Walker features a race of diminutive fluffy bird people who are mostly ultra peaceful and sweet. Mostly. When one particularly xenophobic one gets nasty, he uses his monstrously powerful telepathy to drive an entire invading force of Klingons to suicide, Mind Rapes and possesses Captain Kirk, and almost destroys the Enterprise before he's convinced to stop.
Invasion: Most of the "Furies" resemble demonic creatures (because they're the beings that spawned the legends). A few, however, are fluffy and cute. They're still vicious killers who want their ancestral home back, though.
To Storm Heaven: A B-plot involves Alexander (Worf's son) receiving a hamster from Dr. Crusher as a pet. Worf starts off contemptuous of the sleepy little beast, until he mishandles it and gets the hell bitten out of his finger for his trouble. Worf actually respects its Killer Rabbitness and names it a Klingon name that means "Tribble who battles with honor". Alexander prefers the original moniker of "Fido." Of course, hamsters come from Earth, where most everything not obviously dangerous is probably this trope.
Sten has Doc, an alien who resembles a cuddly koala bear. His species are in fact vicious predators which act cute to lure in prey; Doc is so bloodthirsty that he has to be fitted with a Restraining Bolt in order to interact with his teammates without killing them out of instinct.
Sword of Truth: In Soul of the Fire, an embodiment of evil either possesses or impersonates a chicken. Strangely, the main characters are capable of realizing this... which means you have two badasses who rule the known freaking world and who can alternately make people her slave or destroy armies with a wave of his hand scared shitless by a goddamn chicken.
Tunnel in the Sky: A group of teenagers on a survival-training exercise are stranded on an Earthlike planet when the wormhole they used to get there malfunctions. One local animal is the "Dopey Joe", a stupid, slow-moving cat-sized reptiloid which appears utterly harmless... until the season comes when it, well, swarms.
The Voyage of Máel Dúin: On one of the unknown islands visited by Mael Duin and his companions, the voyagers discover a mysterious palace inhabited only by a playful kitten. Everything is fine until one of them tries to take one of the precious necklaces from the piles of treasure lying around; which is when the kitten jumps at him and burns him into a heap of ashes. Then it goes right back to his play.
The War Against the Chtorr: The bunnydogs appear to be the only friendly Chtorrans encountered by the humans. Unfortunately they also represent humanity's future in the Chtorran ecology: as passive, contented creatures who are glad to be eaten by higher members of the food chain. There are also meeps. A mother rabbit will reject her own young to nurse meeps, who will then suckle her to death. One character darkly theorizes that the excessively cute bunnydogs are meant to be the equivalent for humans.
Watership Down: Gen. Woundwort, who can fight (and beat) many of the beasts that prey on rabbits. As opposed to Bigwig, who is One Badass Rabbit. Also worthy of mention is the Black Rabbit of Inle, the most extreme version of this Trope, since he's basically the Grim Reaper in rabbit-form.
Partway through, White Fang is thrown into a dog-fighting ring. He kills everything sent at him, even a lynx... until the ring owners bring in a bulldog. A remarkably friendly bulldog named "Cherokee" who at first doesn't attack. It nearly kills him.
The weasel that beats up White Fang as a pup is one for sure. The narrator even says that for size and weight the weasel was the most ferocious, vindictive, and terrible of all the killers of the Wild.
The Year Of The Angry Rabbit: Played for Laughs. The novel involves an attempt by the Australian government to cull its rabbit population using an experimental chemical, which results in giant, man-eating (and plague-spreading) rabbits that eventually overrun the continent.