In the Foster's Home for Imaginary Friends episode "Eddie Monster", "the Champ" of the imaginary friends fighting league is a harmless looking Pikachu-esque rabbit thing... that sprouts huge electrified tentacles when provoked.
One episode of Men In Black, in an obvious jab at ET, has a cute and cuddly alien... which could transform into a hideous behemoth on a second's notice when hungry, and was preparing to devour the young boy who had "bonded" with him.
Nibbler of Futurama. It's not his fault he's an unstoppable killing machine... who can devour several hundred times his own body weight in a matter of minutes. His entire species are superintelligent warriors working to save the universe, but it's a Running Gag in any episode they appear in that they're also adorable and cuddly. His very droppings are dark matter more dense than the material in a neutron star.
Several of Stitch's "cousins" from Lilo & Stitch: The Series. Let's not forget Stitch himself, a synthetically crafted living war machine... In a cute fuzzy body. According to Jumba, this was an accident.
Jumba Jukiba: I tried to give you my good looks, but let's face it, something... went wrong.
A Disney Adventures comic showed that this is because somehow the genes of one of the creatures he was created from came from... a puppy.
One experiment was in fact designed to be irresistibly cute as a way of getting into people's homes. He's actually a stink bomb strong enough to cause mass evacuations.
The black hole cousin may look cute, but don't let it open it's mouth.
One of the "Aesop and Son" segments from Rocky and Bullwinkle has a wolf attempting to steal the dentures from a sheepdog in order to render him harmless. After actually managing to succeed, he proceeds to attack one of the sheep, immediately getting fought off by one of the sheep since it also has dentures.
The character Slowpoke Rodriguez is Speedy Gonzalez's cousin, and "the slowest mouse een all Mexico," but he knows hypnosis and carries a .45 revolver.
Bugs Bunny. Once something means war, there's no stopping him. To make that point all the clearer, at the end of this clip there's even an ominous drum boom as he says it.
Droopy the dog looks like he is an innocent helpless little dog, but when he gets angry he will slam the villain to the floor many many times, before tossing them away into something that hurts, such as a cactus.
Tom and Jerry are a cat and mouse who always have something to argue about, including sometimes trying to kill one another over the simplest things; however, in certain cartoons, if there is a bigger problem they are usually working together
Two episodes had Jerry buy a dog that was SMALLER THAN HE IS. But this dog was so fast and violent that Tom was overwelmed. The dog is actually stronger than Tom despite being 20 times smaller.
Nibbler's debut episode had Tom attempt to smash Jerry with a flyswatter, but he accidentally hit Nibbler, when Jerry saw the red sore, he lost his shit and proceeded to destroy Tom for it. This specific line of plot wound up becoming the norm when Nibbler is in an episode, with Tom hitting or otherwise wounding the baby mouse, and Jerry beating Tom into submission for it.
The deadpan little Mynah Bird in Chuck Jones' Inki series. He can demolish anything up to and including a brontosaurus, but always offscreen.
The Dark Lord Chuckles the Silly Piggy in Dave the Barbarian, who is a cute little piggy and a dark lord of evil.
Played rather straight when Pud'n wishes for a cute bunny that will love him forever... and it immediately reveals itself to be a psychotic, murderous nightmare.
Bunny: Some say "love hurts", Pud'n - and I love you a lot.
Also, the Happy Huggy Stuffy Bears, adorable stuffed bears that were created by Eris to sow chaos in the world by hypnotizing their owners to do their bidding. Eris' scheme is undone when one angers Mandy by saying that she'll be only the second most powerful in the world, at which point Mandy orders Grim to decapitate all of them.
Inverted with Billy's "son" Jeffy, a huge, hideous spider who's extremely friendly and wants only to be loved.
In the episode "Dumb Luck", Billy gets attacked by prairie dogs twice. The first time it happens Mandy mentions that prairie dogs take down more people each year than great white sharks.
The Chubb Chubbs, from the video of the same name, are the terror of the galaxy. They look like a combination of the cutest features of piglets and ducklings... except when they're baring their several rows of shark-like teeth and eating barbarian invaders alive. They also enjoy cuddling and karaoke.
Catscratch had an episode which had a duckling in it — and Gordon was extremely terrified of said duckling because of an incident that happened when he was a kitten (the duckling beat the snot out of him with tremendous superhuman strength and horrific fighting skills), but later on Gordon musters up the courage to finally defeat the duckling — after it's beaten the snot out of him AGAIN.
Johnny Test has a cute kitty cat as one of its villains; said kitty cat possesses a cannon that turns people into cats.
The Fairly Oddparents played with this trope as well. The Gigglepies are a race of cute little bunny-like creatures that are a cross between Care Bears in terms of looks and cuteness and Pokémon in terms that they are apparently collectible. They roam the galaxy, coming in cereal boxes and use their cuteness and mind-controlling rhymes to subjugate the population, force them to buy them in excess and eventually cost the planet its freedom. Of course with the Yugopotamians, who fear anything cute, making the populace afraid of them works just as well. Once they're done looting the planet they destroy it and move on to the next one.
"ISN'T THAT CUTE!?" "No! It's horrible! And didn't rhyme!"
A later example is Chuckles the Fairy-Eating Cockatiel, which looks perfectly adorable until the camera zooms out to reveal his full size and razor-sharp fangs. He also shoots lasers.
"Cujo" the ghost dog in Danny Phantom. A small, playful, super adorable ghost puppy... that can turn into a twenty-foot monster who's aggressive meter is off the charts. "Beware of Dog" signs would be an understatement.
Metalocalypse: The band buys an island full of nuclear mutants and converts it into a home for "wayward kitties." The kitties kill everyone on the island.
Ling Ling from Drawn Together, like the Foster's Home for Imaginary Friends example, is an adorable Pikachu-esque rodent... who is also a murderous Sociopathic Hero who kills at the drop of a hat (in the beginning of the show anyway). In just the first episode, he brutally kills and devours another house mate because his name is uttered 3 times. This applies to any of the Pokémon spoofing characters on the show though, as it takes the battling aspect of the series and cranks it up to Grotesque Cute levels.
Ed, Edd n Eddy, quoting Johnny: "I told you bunnies would take over the world, Plank!"
In that instance, the bunnies weren't so much attacking as they had reproduced so much that they flooded the cul-de-sac. A better example would be the rooster Rowlf sics on Eddy in the episode when Eddy loses his voice.
In the The Life and Times of Juniper Lee episode "Welcome Bat Otter", the eponymous bat otter looks like an adorable little otter with bat wings. It's threat level is hyped by the antagonist of the episode, the corrupt businessman mummy Skeeter Khommen-Gettit. It turns out it's threat isn't just hype when it eats Skeeter. The expression on the bat otter's face at the end of the episode hints that its diet isn't limited to evil magical creatures...
Beast Wars had a flower that looked harmless, but got its point across to Proud Warrior Race Guy Dinobot, by nailing him with a spiky seed right where he couldn't reach.
Dinobot: From now on I shoot my dinner salad before I eat it!
"Attack of the Twonkies" says it all in The Adventures of Jimmy Neutron. The Twonkies are essentially dewy-eyed jellybean aliens that turn into evil, spiky, razor-toothed gremlins when they hear music. They can also fuse together into massive red ogre-beasts. And let's not forget the mushroom guardian in "Win, Lose, and Kaboom", a hopping little shi tzu. Sheen in fact attempts to challenge it openly, and it reveals than it can breathe fire. And has piranha teeth. And a prehensile tongue that can supercharge itself with electricity.
The "psycho duck" that Penny Proud adopts in one episode of The Proud Family. It even beat up the Gross Sisters, the neighborhood bullies!
The Pandemic episodes feature giant guinea pigs (which were actual guinea pigs filmed and placed into the cartoon), which are repelled by Peruvian pan flute bands. Several of the guinea pigs wear costumes, such as bee, dinosaur, mouse, and pirate costumes.
Also the Woodland Critters, who seem cute but are actually insane satan-worshipping rapists with demonic powers.
And the cute, little goldfish who wrote murderous messages on its bowl and then followed through with them.
An episode of Eek! The Cat features a cute, seemingly-harmless bunny arriving at Eek's family door, as it turns out the bunny is a deranged psychopath who plots to kill Eek's family after they've thrown Eek out.
The Warners in Animaniacs, three cute "puppy children" who are basically avatars of chaos. And you really don't want to piss off Wakko.
Sabrina's Secret Life. Sabrina conjures up an adorable pet, but Salem discovers that she has actually summoned an evil warlock who is trying to drain her of her powers. Unfortunately, Sabrina does not believe Salem which leads to further complications.
The Snork-Eater-Eater from The Snorks. Said creature was a tiny fish that could open its mouth to a massive size in order to devour the enormous Snork-Eater.
The Wunny Sharbit from Spliced is a cute little rabbit, WITH THE TEETH OF A SHARK AND A CHAINSAW!
The panda pair. Played straight with the panda that clobbered DJ, subverted with the panda that was given to Alejandro.
Any small and cute animal in general, for example, the baby seal. It bites Izzy in the intro.
Plus in "Walk like an Egyptian Part 2", Chef sent scarab beetles after the contestants. Sounds harmless, right? Wrong, a few crawled onto an intern and they ate him alive into just a skeleton in less then ten seconds
Invader Zim has Ultra Peepi, a classroom hamster that Zim affects to grow to the size of Godzilla. Why it grows spikes, has cybernetic parts, and breathes fire is probably Rule of Cool. However, even at his enormous size, with him rampaging the city, everyone stops to say how incredibly adorable is. In one case, as he's using a skyscraper as a toothpick after he just ate a school bus.
Dragon Hunters (Chasseurs de dragons), a French/Chinese cartoon series (plus one CGI movie) produced by Futurikon, has Hector, a blue-furred, dog-sized tame pet dragon with rabbit ears who accompanies the two protagonists Lian-Chu and Gwizdo on their quests and carries their weapons and equipment. (In the world of Dragon Hunters, "dragon" is merely a catch-all term for all monsters of various sizes that are not normal animals.) Hector is often mistaken for a dog by bystanders, although normal dogs do exist too and Hector can walk on his hind legs, has small fingers, is at least semi-intelligent, often sarcastic, and talks in pidgin language. In somewhat of an inversion, while he looks the part of killer rabbit, fluffy but with very sharp teeth and the ability to create small fires and explosions by piddling on things, he is a bit of a coward and serves as comic relief. In one episode Hector meets a fully grown member of his species, Big Blue, who is the size of a house and, while not very aggressive, slowly wanders around the countryside gobbling down everything he comes across in one gulp: whole cows, horses, trees, dung heaps, other dragons, people... Hector on the other hand is thoroughly domesticated; he prefers his food cooked and has shown no inclination to devour actual people.
On Jimmy Two-Shoes, in an animal prison, a fox tries to pick a fight with a chicken. The chicken responds by eating him whole.
Sym-Bionic Titan gives up Mushy/Terax/497, an adorable little alien blob like thing. Did i also mention that when he dies, and no matter how that happens, he explodes with enough force to destroy an entire planet? Yeah.
U.S. Acres has an episode where a little creature named Al wanders onto the farm from underground. He's small, well-mannered, and speaks with a timid voice, but when Orson's evil brothers show up to steal the farm's previous water supply, he drives them off by shooting laser beams from his eyestalks.
In the Samurai Jack episode Jack and the Creature, an annoying but seemingly harmless creature (which even looks a lot like a giant rabbit) hulks out when Jack is wounded by a robot gang. The resultant mutant monster decimates the gang in seconds.
Arguably the Tribe from Jack Learns to Jump Good, once Jack teaches them how to defend themselves.
In Krypto The Super Dog, Mechanikat's minion Snookey Wookums, though cute-looking, is a cunning and vicious little thing.
In The Twisted Whiskers Show, a kitten named Cutie Snoot, although cute and sweet, she causes trouble for a dog named Goosers to earn the affection of her master.
Snarf from Trollz is an example of this. He normally appears as a red cute-looking puppy/wombat creature, but get him mad and he turns into a vicious, hulking ogre.
Sponge Bob Square Pants has "Puffy Fluffy," a cute and docile little critter...unless you piss him off, which is when he turns into a horrific abomination with multiple Sarlacc-like tongues. Whatever you do, DO NOT put him in a house with another pet.
A couple Transformers continuities feature Scraplets. Oh, they may look like cute little toys, until they sprout rows of sharp, metal teeth. Then they prove how good they are at swarming, and therein have been shown to take an entire Insecticon apart in seconds.
When Count Duckula asks a spaceman to take him to the most dangerous planet in the galaxy he gets to meet the Fluffy Bunnies of Planet Cute, who want everything to be sweet and pretty and cuddly, and get very mean when Duckula and co. persist in being grouchy and sour.
Snarf of the original ThunderCats. He may be small and his "cute" factor may be up for opinion, but on three separate occasions he's pretty much the last one standing of the Cats — and rises to the challenge, tilting the balance enough to win the day: "Snarf Takes Up the Challenge", "The Wolfrat", and "Psych Out". And just try to threaten Lion-O, even after he's all grown up.
In Generator Rex, Rex arrives to defeat yet another monster only to somehow only see a small rabbit; as somehow he lacks a sense of perception and is color-blind because after he insults rabbits, the rabbit hops up to him where it is clearly seen as over 3 metres tall, six-legged, razor-toothed, and blue furred. It then menaces him randomly for the continuing week (i.e. while he's watching a movie, playing basketball, walking down the street).
Being the element of stubbornness and brute force, you wouldn't expect the most powerful Earthbender to be Toph, a tiny blind girl.
My Little Pony has a benevolent example with the Flutterponies. Despite being...well, little ponies with Butterfly wings, they're the ones the heroes seem to turn to when they're completely outmatched, and for good reason, as the Smooze and Erebus, two of the pony's strongest enemies, found out the hard way.
All of the ponies across the franchise count as this, really. They're small technicolor horses with pictures on their rumps that live in magical worlds that include plenty of entries from the Monster Manual. While they often try to talk their enemies down, if that doesn't work, they defeat them.
If you want a specific example, you need go no further than Fluttershy from Friendship is Magic. She's considered cute and harmless even compared to the others. It's next to impossible to provoke her into a fight, but woe be to whoever tries to harm her friends or her animals.
The Cutie Mark Crusaders are a trio of fillies who haven't even earned their cutie marks yet and tend to spend their days on wacky adventures trying to earn them. Cute, yes. Harmless, no. When Babs Seed pushed them just a little bit too far, they cranked the A-Team music and built a trapped parade float rigged to go careening off a cliff (using an egg timer), then tricked Babs into stealing it with a Batman Gambit. Also, of the three Sweetie Belle has also shown to be a serious manipulative bastard in training.
Gen 4 Spike is still a baby dragon, generally harmless unless defending a friend. However, when his greed takes control and induces Rapid Agingthings can getdangerousfast. Even as his normal self (despite being a baby), he's still a fire-breathing dragon who's brave enough to put himself between a timber wolf (a massive monster made of wood) and one of his friends and take it down.
A literal (if downplayed) example, would be Fluttershy's pet rabbit Angel. Cute yes. Nice. No. He once threw Fluttershy out of the house over missing one ingredient on an elaborate salad.
Geshie the mascot from Genetically Engineered Superhuman High in Clone High.