In RuneScape, the player is required to get rid of a "giant wolpertinger", and says that it is just a "harmless wee rabbit". Subverted of sorts when it turned out to be a dangerous and heinous monster.
Fantastic Dizzy has cute little snails. Yes, snails. These loveable, unkillible, little geranium-munching monsters are really good at chipping away at your health normally, but if you drop from any ledge on the right-hand side of Dizzy's village you risk the humiliation of being stripped of your entire health bar in moments as one cheerfully and aimlessly wanders past Dizzy while he is stunned. Do not mess with the snails.
Several of the weaker Heartless fall under this, especially the Shadows, which are the first type of Heartless that you encounter in the original game. They may be Made of Evil, but they're still adorable.
Wyverns too. Yes, they're man-sized dragons, but they're very cuddly-looking man-sized dragons.
And in the prequel game, Birth by Sleep, some of the Unversed may or may not qualify, but they also notably feature a literalKiller Rabbit amongst their ranks, called (amusingly enough) the Hareraiser, which is described as being "the anti-cuddly".
Most of the Dream Eaters in KH3D fall under this, being stylized, colorful versions of real and mythological animals which more often then not look and sound adorable, but are no less capable of murdering you (or your enemies, for that matter) than the previous enemy types in the series. This applies more to the friendly Spirit Dream Eaters, as the evil Nightmares have red eyes and dark colors that make them look more threatening. Again, there are literal examples in the Me Me Bunny, a ridiculously cute rabbit Dream Eater that beats up its enemies with its ears, and its Palette Swap Majik Lapin, a Robe and Wizard Hat-wearing spell slinger.
In the plot, one Nightmare Me Me Bunny summoned by Musketeer Pete takes out Sora in just one hit. It even makes an adorable cry at the moment of the strike.
An almost literal example from Odin Sphere is Prince Cornelius. He looks all cute and stuff, but easily he'll hand you your ass with his Zero-like fighting style.
The slimes. Most of them actually aren't that dangerous, but given how incredibly adorable and harmless they look, it doesn't take a lot for them to be much more dangerous than they look. Tell me you'd think this could do any harm.◊
They're far from the only cuddly-looking killers in the series, though. Quite possibly the best example would have to be the Sanguini family, which are cute little baby demons. So cute, that one optional quest has you fulfilling the request of a warrior who is smitten with them to deliver each type a scarf. Awwwwwwwwww. That said, aside from wasting turns "fluffing around", they can be dangerous. It's pointed out in the Flavor Text that Manguinies, the genuine, demonic looking...demons, are the result of a Sanguini that has drank enough blood.
Rabites, which are sort of blobby killer rabbits◊. Although the yellow ones are little more than a nuisance, even to a small child, some of the other colors really are quite dangerous, especially the black ones.
The Black Rabite, one of the adorable little creatures mentioned above, with the respective color, is the most dangerous thing in the game. It looks like a small black bunny slipper until it opens a can of whoop-ass on you. The Black Rabite can be tamed a great deal by avoiding the use of spells or any tech stronger than the basic one, as these will not trigger its ferocious counterattacks. It also helps to use stat-affecting magic like the Necromancer's Black Curse spell and the Nightblade's Deadly Weapon spell.
The Fairy you can recruit in Romancing Sa Ga 3 is a very versatile character, good with Spears, and Bows.
The knife-carrying, explosive and possessed-by-the-souls-of-criminals penguins known as Prinnies from most of the games since Disgaea: Hour of Darkness. And as if the regular ones weren't bad enough, the final ultimate form of Overlord Baal, the most powerful Bonus Boss in all said games is a prinny as well.
Starting with Dark Hero Days, the position of most powerful bonus boss has been usurped by Pringer X, a tiny robotic Prinny that doesn't look threatening, aside from its red angry eyes.
Before even prinnies, we had Eryngi, cute little mushroom creatures that call up mushrooms to attack and say 'gii!' a lot. One of them actually demands that you kneel down and beg for your lives lest "your blood will rain on me, gii!" I don't need to say who. Another Eryngi appears in Disgaea 4as the True Final Boss. It is also a god.
The Catsabers, present in multiple Nippon Ichi games, resemble children in cat costumes, but are generally no less deadly than any of the other species of monsters you're likely to run into. They also have a more diabolical relative called the Deathsaber, with an appearance resembling a bat, rather than a cat.
LittleBigPlanet: Sackboy. He's adorable, perpetually happy and silly, and wants to pal around with his friends. He's also a reality altering super-powered entity who can create whole worlds with pure thought, alter the state of any object, fly, control time, and has a mean right hook.
The Legend of Kyrandia series has the Kyrandian Killer Squirrels. In the third installment, Malcolm's Revenge, there's one on the very first screen—allowing you to produce one of the fastest Game Overs in video game history, simply by teasing the squirrel twice—at which point it'll leap at your face, kill you, and drag off your corpse to feed its young.
The Tonberry (normally encountered alone) is so dangerous that, when facing three of them in Final Fantasy VI, they are actually classified as a different creature labelled "Tonberries", just so you know what you have gotten yourself into.
Also apropos to this, Final Fantasy XI features a number of cute-but-deadly monsters, including rabbits, composing families with level tiers reaching up to very high levels in most cases. Rabbits are one of the more powerful mob-families in general, leading to the saying: "No matter how powerful you are, somewhere in the world there is a rabbit that can kick your ass."
The cute fluffy and peaceful animals are also quite frequently the most dangerous mobs in a region otherwise populated by undead horrors and other things that at least look threatening. As new players get told, never anger the cute little things or you'll find out why the scary big monsters would rather fight you than them.
From the same game, the Tarutaru race are adorably short and cute; with adorable pointed ears and button noses to boot. They're every bit as powerful as any other player race, though, and especially skilled in magic. Of particular note is NPC Professor Shantotto, who flat-out scares a good number of the heroes and villains in Dissidia: Final Fantasy.
Mog from Final Fantasy VI can do quite a bit of damage with his dances. This◊ ad◊ for the SNES version of the game is a bit of an exaggeration, but just a bit...
Final Fantasy XII has several classes of cutesy enemies, including mandragoras, onions, cacti, and the insanely fast and surprisingly powerful Dreamhares, who actually look like rabbits. The cute enemies your party encounters early in the game generally will not attack unless you attack them first, but later versions are more hostile and can inflict lots of nasty status effects. The king of them all is Fury, a cute little boss bunny who lives in the Necrohol of Nabudis. There's also one literally called the Vorpal Bunny. It's a rare hunting Mark, meaning it's not QUITE as tough as Fury is, but stil nothing to underestimate.
There is also a sidequest where the player must alert a troup of dancing moogles that their seeq boss plans to sell them. The moogles respond to this revelation by beating their boss to within an inch of his life.
The bunnies (okay, "Dreamhares") in Final Fantasy Tactics A2 aren't all that killer—they can mind-control your allies, but they're easily set on fire. In one mission, however, you encounter a slightly odd-looking variant of the species deep underground, and one of your moogle allies shakes in fear at the sight of it. Turns out it's a "Mooglebane," named for its favorite food. Fury, mentioned above, also makes a reappearance in this game.
Cactuars. They look like cute little cactus people. but they have a Fixed Damage Attack that can deal 1,000 damage, no matter what. Even worse is that some games have a second version that can do 10,000 damage, more than the normal HP cap, meaning instant death to anything it hits.
In Final Fantasy V, there's a cave where you are attacked by "nut eaters"- squirrel monsters, who are not very dangerous, having only 1 hit point each... but frequently, you'll run into a "skull eater" instead, which looks identical (except for being black) and who is powerful enough to kill your whole party! (Ironically, it still only has one hit point, so if you manage to penetrate its defense, it goes down in one hit.) Not to mention that if you try to use magic against it, not only will it not work, but you'll now be faced with five of them! The Updated Re-release introduced another Palette Swap in the Bonus Dungeon, called Soul Eater. However, this one is more like a Demonic Spider, nasty but doable without special tricks.
Chocobos can take you to school too. Not so surprising really, with those big clawed feet. Taken Up to Eleven in Final Fantasy XIII with Sazh's pet baby chocobo, who is not only insanely intelligent, but takes out an armed soldier by itself.
The Red Chocobo in Final Fantasy Tactics can do all the things a normal chocobo can do, and of course, summon a fiery meteor of death.
Final Fantasy IX: Yan. They're so adorable... but they're the strongest monsters in the game, and can easily take out a full party in seconds with Comet, which they will take full advantage of, Virus Power, which will prevent the afflicted from gaining any EXP you get in the battle, and has Float/Snort combo, which blows away one of your party members and counts them as Dead.
The Cuccos in The Legend of Zelda games are perfectly harmless chickens for the most part. If attacked, though they are clearly being hit and react with distress, they suffer no ill effect. If attacked persistently, the Cucco will begin to hit back, and an endless swarm of other, equally invulnerable Cuccos will come to its aid, pursuing the player and attempting to peck him to death.
Their chicks are also masters of deception. In The Minish Cap, the bouncing yellow babies with their cute chirping noises appear to be completely harmless. That is, until you turn Minish-sized and enter Anju's house, where about fifteen or twenty chicks will take notice of you and chase you around in an attempt to eat you. So, essentially, this makes Link...a chick magnet.
In The Legend of Zelda: The Wind Waker, there is a black pig that you can give to a family near the beginning of the game. When you come back to your home island, it will have grown huge. It is possible to jump in the pen and attack it until it becomes hostile, but this is a very bad idea. It will cause three hearts of damage when it hits you, which is more than any enemy in the game can do, you can't block it, and it will keep ramming you until you jump out of the pen.
In Skyward Sword, they've got those little cat-raccoon-pet-things in Skyloft called Remlits. During the day they meow, follow you around, and look absolutely adorable with those huge Bambi-eyes. During the night, they're actively trying to rip your guts out. This is actually because they've been corrupted by a demon. Turning the demon human causes the Remlits to retain their much nicer natures at all hours of the day.
In Mortal Kombat: Shaolin Monks, there is a secret, unlisted move called Unfriendly Rabbit, which is simply murderous. The enemy just sits there and pets it while you get the hell back, and then, out of nowhere, the little lagomorph suddenly tears into the enemy. When it says Fatality, the rabbit pops out of the enemy's... maybe it was stomach. Then it sits there as if nothing happened.
And Kung Lao can use a bunny to beat his enemy to death. These are based on Kung Lao's Friendship where he pulls a bunny out of his hat. Only here, it's turned into a Fatality.
In the MMORPG Asherons Call, the second most powerful monster in the entire game was the level-666 White Rabbit, nicknamed "Pookie" by players. It was not uncommon for Pookie to slaughter entire parties of high-level characters using spells such as "Bunny Smite".
In the secret quest of the first game, you fight Killer Chickens.
In the secret quest of Dungeon Siege II, you fight Killer Prairie Dogs.
Many Pokémon would fall under this. For that matter, many Mons series critters and cute anime mascots fall into this trope.
Several of the incredibly powerful "legendaries", like Mew and Jirachi, are certainly small and harmless-looking. However, in the game, Mew has good stats and can learn every available technique. And Jirachi has a powerful Steel-type Signature Move called Doom Desire, which lets loose a devastating bundle of light on the foe.
There are so many that they form a category themselves: the "Cute" Legendaries. Most of them have stats above the average end-game 'mons, and have moves or abilities that make them utterly devastating. Those who aren't are no slouches either.
The only Pokemon that can learn Metronome, an attack that can randomly use nearly any move in the game, by level up are cute Pokemon. "Togepi used Metronome! Togepi used Fire Blast!"
The best example would be the Mystery Dungeon series. Since you are not allowed to evolve your main character until the post-game, the final battle will always be something on the lines of two tiny, cuddly starters punching the crap out of the resident Olympus Mons.
The sixth generation introduces the Fairy type. The type even sounds cute, and plenty of its members certainly are. The type is super-effective against the Dragon type.
Mawile's Pokédex entry states that it lulls its foes into letting down their guard with its cute face, and then attacks them with its huge jawlike horns.
All starter Pokémon start out cute and relatively weak, but evolve into something more threatening, and later evolve again into a huge, terrifying, powerful beast. Most other multi-stage evolvers follow this pattern.
A literal example in Pokémon is Azumarill. It was a Joke Character when it was first introduced, but four generations of badass levels have turned it into one of the game's premiere dragon slayers.
Another literal example is Diggersby. It is often dismissed as a trash Com Mon, but if it has Huge Power (The same ability that makes Azumarill so potent) as its ability, its attack can surpass Groudon's attack.
The game features an enemy that looks like a teeny-tiny green ball (described as a plant in the manual). Approach it and a gigantic mouth extends from it, killing you instantly — although if you know what you're doing, you can paralyze it in the split-second that it takes for the mouth to reach you.
There are actual deadly living rocks in the game, and plenty other creatures that look either goofy or cute, but can kill you with a mere (venomous) touch. Or by breathing fire. Or pushing you into a death trap. Or gobbling you up.
In the MMORPG EverQuest there are certain fish considered sacred by a god. A god who sometimes poses as one of the fish. Attack them at your extreme peril.
This trope was parodied (before the Cataclysm) in a Warlock class quest. After fulfilling the desires of a clearly insane Gnome warlock NPC, he attempts so summon a powerful demon... but gets a giant chicken named "El Pollo Grande" (The Great Chicken) instead which, despite its appearance, isn't much a challenge.
Some gnome players. Yes, they may be small but that means they have the smallest game avatars to target and can pack the same punch as their peers in terms of class and level.
And then there was the accidental Bear Reaver. Normally, a bear isn't that small and non-threatening, but when that model accidentally, in a Beta realm, replaced the gigantic Fel Reaver model in Hellfire Peninsula, and the thing went around looking like a medium-sized, low-level beast but still shaking the ground as it walked and remained capable of killing players with one hit, that sounds like an example of this trope.
Engineers can make a device called an Explosive Decoy that looks like a rabbit and just hops around a bit; if attacked, it explodes.
The second tier of Brawlpub has the penguin Dippy, who waddles cutely after the player, and falls cutely to the ground when hit with a direct-damage attack. It can't be rooted or slowed, however, and if it manages to get close enough to the player to use its Peck ability...
The elementals of Pandaria are adorable, but they can be deadly when provoked. Special mention goes to the ones on the Timeless Isle who can take off one third of your health with their attacks and Lei Shi in the Terrace of Endless Spring.
Scarfy. Try to have Kirby inhale this cute little cat, and he gets ugly and chases you around until he explodes.
Pretty much every enemy in MapleStory falls into this trope. As a rule, the cuter the creature is the faster it will kill you.
There are tons of high-leveled monsters that would like to object to that, but examples do exist, especially when low-leveled. See: Slime King, Mushmom, (Dark) Yeti and Pepe, and Bob the Snail. Be especially careful with that last one.
A more recent addition is Pink Bean, a pink, Pikachu-like boss that eats, sleeps, and plants flowers during the first half of the fight, and then starts killing half of your party members off in a single attack.
The Elemental Kittens of Doom (Jr. Cellion, Sakura Cellion, Jr. Lioner, and Jr. Grupin). They act all pathetic when getting beat up and all but they mob like crazy and can spell doom for those who are more than a few levels below their Level 33.
The Rabbids from Rayman: Raving Rabbids aren't quite literal killer rabbits (their violence tends more towards slapstick Amusing Injuries), but they're still violently insane and insanely violent. And they're trying to take over the Earth and television. They're succeeding.
Back when Rayman: Raving Rabbids was going to be a platformer, the Rabbids were going to be hideous, vicious, and downright horrible creatures, instead of the insane but humorous critters they are today.
The Memaus in Startopia are cute little cat-like creatures that wander around the station. They eat litter, and any guests who pet one get a bonus to happiness. The problem is that, if it's been well-fed, it simultaneously infects the petter with a parasite which will transform the guest into a decidedly not cute "Skrasher" which cuts a swathe of destruction and can absorb a terrifying amount of damage before keeling over. And if your security can't kill the Skrasher fast enough, it explodes... into more Memaus.
EarthBound brings us the Clumsy Robot, whose combat actions include sweeping up dustbunnies, picking up nuts and bolts that jiggled loose from its body, eating bologna sandwiches, accidentally firing party-devastating beams and missiles while tripping over its own two feet and being completely unkillable by all normal forms of attack. The party eventually has to be bailed out by the Runaway Five...who simply run in while it's distracted and turn it off.
Ratchet. Small, fuzzy, and carries around more firepower than even the Pentagon could dream of.
Also, from the second game in the series, we have the Protopets — cute, Tribble-like critters that have rows of shark-like teeth, a nasty temperament, and the tendency to eat anything or anyone they encounter. Oh, and they have the reproductive ability of the original Tribbles as well.
The Precursors from the Jak and Daxter games, the most powerful beings in the universe, are revealed towards the end of Jak 3 to be Ottsels, just like Daxter. Ever wondered why you never saw one?
There is a part in the level "Down The Tubes" where you ride on top of a huge hamster that can eat pretty much anything. And that's the least of the harmless-looking things in Earthworm Jim that can beat you to a bloody pulp.
On that same level are small red creatures about half the size of Jim that resist gunfire and if he approaches too close, they slam him against the ground.
In a later level, a slime-dwelling creature dwells at the bottom of a massive chasm that looks like a little tan balloon with a smile unless you get too close to it. If you do, it will swiftly start to resemble a tyrannosaur.
Then, of course, there's quite possibly the reigning king of this trope (screw seniority) Peter Puppy. A little, pink puppy who, if he gets hurt, changes into a massive, purple, spikey monster with lots of teeth and drains a third of your heath as it literally chews you up and spits you out.
Similarly, in another one of tri-Ace's games, Star Ocean: Till the End of Time, the Sooties (little balls of soot with eyes) are by far the most difficult regular monsters you'll ever meet. They're insanely fast and strong, and due to their tiny size are really difficult to hit. Incidentally, the first Star Ocean includes a "Vorpal Bunny" as one of its enemies. Though it does look cutesey, it's also twice the size of a human, so not all that cute.
This is pretty much the entire point behind the Gaia Online MMO: zOMG!. Yes, that is actually the name. The basic plot is that relatively harmless inanimate objects such as garden gnomes, cotton balls, and cloves of garlic are somehow becoming animated. A literal case of Everything Trying to Kill You, if you will.
The result can be best summed up in a promotional poster featuring a musclebound, heavily armored Orc trapped up a tree by a Lawn Gnome, "Cute? Cute never tried to eat your leg."
Not to mention those damn Cherry Fluffs, toward the beginning. After easily dispatching three other varieties of Fluffs, you might try your luck on one of these pink fluffy whatsits, only to have the entire thing blow up in your face.
Braid: Killer Rabbits squared. Or cubed. Not only are these rabbits vicious, but they initially disguise themselves as flowers and sound like cats. No matter what you find cute and charming, there's a good chance Braid's rabbits will undermine it.
One exception: Mist from Path of Radiance. She looks no more than a petite 13, can't fight until she gets a class change, and then deals substandard damage. Not quite as young or ineffective in Radiant Dawn, but still unimpressive. She's far from ineffective though, although it takes a bit of work and luck, she can be capable of almost soloing whole maps thanks to her high luck.
The MMO La Tale has so many of these that a good rule of thumb is "if it looks cute, run like hell." Especially annoying are the Prring Palette Swaps and Shaggies, which mob you and jump behind you to deliver devastating back attacks.
Kukuri in Magical Battle Arena. She's a Super-Deformed sorceress that uses hilariously cute spells and out-adorables every other character by miles (which is saying something since this game is filled to the brim with Magical Girls), but good grief, she is deadly. Between the strawberry firing Strawberry Snake (read: Machine Gun), the smiling pink Mini-Planet (read: Gravity Sucks Mines), and the cat totem-pole Long Voiced Cat (read: Mana Drain), all of which she can cast nigh-instantaneously, she's a deceptively dangerous fighter in the battlefield.
Near the end of Wizardry VI: Bane of the Cosmic Forge, you may run into faeries in the same areas you're routinely facing down dark crusaders, greater demons, elite samurai squads, and mind flayers. The faeries are much more dangerous than any of the enemies just mentioned, and indeed one of the toughest enemy types in the game. Just be glad these unassuming Demonic Spiders don't show up until around the final dungeon.
Perfect World has antelope. They look almost harmless compared to the typical werewolf or protoplasmic ooze, but they are both aggressive and equipped with a dangerous Mana burn.
Every single monster in the obscure Game Boy Color RPG Lil Monster is like this. Although some of them are meant to be fierce and imposing, every monster in the game is rendered in a cute, Super-Deformed style. Even the final boss, portrayed as a kind of Eldritch Abomination, still has a head that's half the size of his body and dewy eyes.
The Hairy Bulborb from Pikmin 2 has huge blue eyes, a tubby round body, and is covered all over in incredibly soft-looking white fuzz. It's downright cuddly. However, as with any enemy in Pikmin games, if you so much as look at it wrong, the Pik-carnage will be endless.
The Liir from Sword of the Stars are a playable example. They look like friendly whales and dolphins, and are, whenever possible, Actual Pacifists. However, if you push them to the point that this is no longer possible, it can easily lead to bad things. The game's resident Abusive Precursors, the Suul'Ka did this by enslaving the Liir and threatening to pollute their oceans to an uninhabitable state. There are no more Suul'Ka in this sector of the galaxy, and possibly in the universe; the Liir used their talent for biotechnology to wipe them out with a genetically engineered retro-plague.
You know what rabbits stereotypically like to eat? Carrots. However, as anyone who has ever played Mushroom Men can attest, this is a damn lie. They actually enjoy eating tasty little mushroom boys. Take one step toward one of those Green Rocks-possessed, lapine monstrocities, and just watch how fast you die.
The Rampage Rabbit from Summon Night: Swordcraft Story 2. After you beat it the first time, it trains itself so that it can beat you afterwards, and is aiming to be the most powerful rabbit.
Minecraft has a literal example of this trope in 'The killer rabbit of Caerbannog' that was added during the bunny update. They're incredibly rare, having a one in one thousand spawn chance, but they're incredibly dangerous. Without armor, they do seven hearts of damage.
The original game brings us Anti-Guys, who merely appear to be Shy Guys dressed in black. However, they possess boss level HP and have an extremely high attack power, being able to cause as much as 12 damage per hit. Fighting them is completely optional, however. The first one seen is guarding a chest and can be bribed with a piece of candy, plus he'll specifically warn you multiple times about picking a fight with him. You can later get three of them sicced on you as punishment for failing a minigame, and it's easily the hardest fight in the game.
On the topic of the Paper Mario games (first and second), Amayzee Dayzees. Cute, shiny anthropomorphized flowers, have a tendency to just run away from the battle... and when they don't, WATCH OUT!!! 20 HP, 20 attack, and 1 defense. Good luck taking one out, as it'll either run before you get the chance, or kill you.
In Dark Cloud 2, Dark Emperor Griffon's true form is that of an adorably cute bunny person. Even the protagonists are surprised. But then the boss battle starts, his true skill as a master mage surfaces, and the infinite power of his Cosmic Keystone shines forth. Hint: Max and Monica embody the Earth and Moon in their Atlamillia. Their foe wields the Sun.
One of Metal Gear 2: Solid Snake's most Guide Dang It obstacles is the MSX cartridge guarded by 'deadly poisonous Zanzibar hamsters'. At this point, Snake's life bar is as long as it can get, and he has shot down a Hind D helicopter, and Metal Gear D's guided missiles only take off about a sixth of his health bar, but touching one of the tiny brown rodents causes instant death. That said, they die in one hit, so once you've worked out the puzzle to lure them from their hiding place you only need to stand in front of the hole and fire.
The Mimigas, friendly anthropomorphic rabbits that are your main allies throughout the game. But, give a Mimiga a red flower to eat, and... they enter a "frenzied" state, which means they mutate into horrific, bloodthirsty, mindless monsters that simply kill and kill and kill until they die. Even the weakest Mimiga becomes powerful enough to be an early-game boss in this form. The Mimigas are aware of this power, but only use it as an absolute last resort.
And then there's an optional late game boss, Ma Pignon, which is a small, smiling blue mushroom. A smiling blue mushroom that begins rocketing around the room hard enough to cause landslides to fall from the ceiling.
Dwarf Fortress Wiki: [T]here is only one thing to do if you come across a river full of carp and you don't want your dwarves to die... Run. Run and never look back. Toady One:I think I made the fish too hardcore.* No, that's not a sinkhole. It's not our own attempt, and it IS an understatement.
Carp have stepped down from this position in favor of giant sponges, which will kill your dwarves if they get close to it. Not bad for an animal who shouldn't be able to even move. This deadliest arises from two things about the sponge; firstly, due to having only one body part, its effectively invincible to brute force. While it doesn't chase your dwarves down, if its located in a river, it's bound to cause mass job cancellations. The deadly part comes in when one realizes just how heavy giant sponges are; even with the pathetic push attack that a creature with no natural attacks receives, a giant sponge can easily shatter a dwarf's spine. If you ever encounter the elusive vampire giant sponge, which can not only move but can also leave the water, may the gods protect you.
Also, giant keas are rampaging homicidal kleptomaniacal psychopaths, in the form of parrots.
Also, at least one fort has had an incident where a wild duck battled The Legions of Hell and defeated two demons by itself.
Elephants themselves have this status. In real life, elephants are animals who mind their own business and tend to shy from civilization unless necessary. In Dwarf Fortress however, elephants are insanely territorial, fear inducing death machines fueled only by their burning hatred of dwarves. Most famous in Boat Murdered.
The Chichifa from Star Flight 2. You never see a picture of them. But the Humna Humna trade buoy orbiting their homeworld describes them as "A race of highly prolific, small, furry creatures with long, upright ears and puffy tails. Extremely aggressive, they will swarm to any heat source and attack. Recommend caution."
Baragon in the game Godzilla Unleashed certainly applies... even if he is a giant dinosaur-thing. Sure, he's the smallest monster in the entire game, and he is adorable in an odd sort of way, but he's more than able to take down his opponents including the biggest monster in the game, Biollante.
In the Guild Wars: Eye of the North expansion, the player can be lured by a cute little bunny into a small hollow filled with cute little bunnies... that then turn into a LOT of nasty Vaettir with a named boss in their midst.
And in Nightfall, we have the beetles, basically spherical creatures that move by rolling around and make pretty cute noises. While the original beetles are a nuisance, the Madness titans later on can mess your party up.
There's a Killer Rabbit terrain in Populous. Piglet World is a land of pleasant, grassy meadows and flowering trees... and is apparently so deadly that your little piggy people will start dying immediately after leaving their homes.
It is canon in Touhou that on the moon is an entire race of humanoid lunar rabbit youkai that make up most, if not all, of the moon's army. This in essence plays it straight almost completely literally, but at the same time somewhat subverts it as they act like rabbits, lazy, carefree, and fun loving, so aren't quite as deadly as they could be. Though still deadly.
According to Hieda no Akyuu, to some people, KazamiYuuka just seems like a polite but weak flower youkai. She even includes a nice, peaceful looking picture◊ of her. Akyuu goes on to assign her a threat level of "Extremely High" and a human friendship level of "Worst." Given that Yuuka has claimed, sincerely or otherwise, to consider genocide a game, this might not be an entirely unreasonable assessment.
Quest for Glory IV has actual killer rabbits. Then there's the old lady's pet kitty in the first game, if you're a thief. And those pesky antwerps...
When you finally catch up to the Girl in Black in Persona, she pulls out Tesso. It's a giant mechanical rat that makes cat-like noises. Any females in your party will squee over it... until it opens fire. Kei then mocks them for falling for it. Tesso's the boss of the area.
Gameplay example in The King of Fighters. Hotaru seems harmless and in terms of personality but is a monster in the hands of a skilled player (and is generally high to top tier).
While headcrabs in Half-Life are generally not considered cute, with the possible exception of Lamarr, they fit this trope by being small, innocuous, apparently harmless, and by far the most horrific thing in the series, latching onto an unfortunate host and commandeering its nervous system to create a delightful monstrosity known as a headcrab zombie. And the Fast and Poison variants are even worse.
From Half Life Opposing Force there's the Spore Launcher weapon: An infantile alien soldier that spits explosive spores at your enemies. An absolutely adorable idle animation has Adrian petting it, which it happily accepts.
The most powerful nature summon is an ordinary white rabbit. And by "ordinary" we mean that it's called a vorpal bunny. It is level 50 (with level cap being 55) and can be summoned at level 5 with right character. At this level (and for the most of the game) it tends to invoke Chunky Salsa Rule in a single bite. And you can have several of them. And they gain levels if you don't unsummon them.
Also in Arcanum is the Stillwater Giant, a brutal and deadly monster whose default form is a small blue rabbit. Even if he loses to the above in one combat round.
With enough modification, Forza 3's 1964 Volkswagen Rabbit will eat Ferraris and Lamborghinis and crap them out as Yugos and Trabants.
Toon Link also could count. He's a cute-looking kid with a toy sword who can also kick your ass eight ways to Sunday with an array of weaponry (and the skill to use it) that's just as impressive as his adult self.
Jubei from the BlazBlue series is a traditional nekomata, appearing in the form of a small two-tailed cat that stands upright. He also happens to be one of the six heroes, carries the most powerful katana in the world (the Nox Nyctores Musashi), and is stated to be the most powerful living creature in existence. To give you an idea how strong he is, he turned back Iron Tager's attack effortlessly, and Tager outweighs him by about a ton.
Ys: The Ark of Napishtim has Majunun, a cute little robot so comically tiny he's not actually visible in most screenshots of him. It's a lie to say he's the most powerful boss in the game — "most powerful enemy, period" is more accurate, as he technically only counts as a miniboss. He's capable of one-hit-killing a Level 31 Adol... and to get one useful accessory, you have to either kill him, or manage not to be killed by him long enough to grab the chest and escape.
The eponymous Metroids themselves are an inversion of the trope, since your first impression is how deadly they are, but if you come across one that isn't trying to consume your soul... d'awwwwwwwww. They're typically babies when encountered, make an adorable chirping sound, eatnote you by glomping, and if you're lucky enough to have one imprint on you, you don't even need to stick your head between your legs and kiss your arse goodbye.
Metroid: Other M gives us "Little Birdie", a little white fluffy thing that looks sort of like an armless mouse standing on chicken legs. It was considered to be a failure as a bioweapon, so the scientists kept him as a pet. And then it ate one of them. To be fair, it should have tipped them off with its malevolent, soul-piercing gaze.◊ And it wasn't a failure at all. The scientists who cloned the Space Pirates didn't realize that Ridley had a larval stage.
Both chapters of SSI's Wizard's Crown duology featured these, as "white rabbits" in the first game and "snow rabbits" in the second. In the former case, they're a set-piece encounter more dangerous than just about any other pure-melee opponent in the Ruins, and provide a ridiculous quantity of high-quality loot. In the latter, they're wandering monsters in the toughest of the three wilderness areas, so their lethality is rather less inappropriate.
Little Mac from Punch-Out!! is roughly half the size of the majority of his opponents, yet he can throw lightning fast punches so powerful he can topple them with ease.
Gharbad, the Goat boss from Desktop Dungeons, appears relatively harmless. Then you see his Base Attack. He has an attack score of 255. Nothing else in the game comes close. Unless you have some way to kill him indirectly, you've lost.
The appropriately named "Double" from Mega Man X4. He's a short, round, inoffensive-looking reploid who's only about as tall as X (Read: short) and his only job on the base teeters between radio-operator and janitor. Then he reveals himself as The Mole, grows to about three times X's size thanks to the Shapeshifter Baggage stored in his "stomach" complete with Wolverine-claws and a complete Evil Makeover, and gives X one heck of a nasty fight.
Mega Man Zero 3 has a literal example with Childre Inarabbita. His battle form is that of a rabbit, and his humanoid form, is that of a child. He's also one of the Eight Judges that govern The Empire alongside X and his Fake King replacement.
In the Terra Tubes of Battletoads, there are enemies that look like rubber ducks. Not only are they vicious menaces, they cannot be killed, only stunned.
Similarly, in the Ice Cavern, there are Snowmen who throw snowballs at you for one damage... but get take too long killing them and they knock you out with one punch. Not as nasty as the Rubber Duckies, but then it's not quite as cute either.
The final boss of Let's Go Jungle! is a giant killer butterfly. Because after all the other giant creepy crawlies in this game, why not butterflies?
Deepstalkers from Dragon Age: Origins are surprisingly cute for a bunch of flesh-eating, poison-spitting, lamprey-faced compies that burst from the ground in the dozens hoping to tear you limb from limb.
The baby dragons are almost too adorable to kill.
And in Awakening, Anders tells the tale of his pet cat back in the Circle Tower, Mr. Wiggums, who was possessed by a rage demon and killed three templars.
A long-standing joke, even with the creative staff is that your pet Mabari's name actually is Rabbit.
The games have the Djinn, cute little elemental Mons that you find and collect for stat boosts, Summon Magic, and class changes. Some of the Djinn have to be fought and subdued before they join you. These are the ones that will use high-end Psynergy attacks and are effectively minibosses.
Divinity II: The Dragon Knight Saga has the Killer Bunny, which appears if you kill enough bunnies. It has huge fangs and blood-mottled white fur, and is level 22. A particularly sadistic player can encounter it very early when they're likely dangerously underleveled, and score a massive XP reward... or, more likely, a brutal death. There's a special achievement for killing it, too.
With no exception, whenever you come across an opponent that looks small and cute, you'd better be prepared for a long, horrible, grueling and deadly fight. The dialogue in the game is rife with enemy descriptions saying, "this little creature looks harmless at first..." whereupon it proceeds to shred and/or cremate your ass big time. In fact, small creatures in this game are usually much, much tougher than most of the big and scary opponents due to the fact that they are usually given incredibly high evasion stats. Basically, if you come across an enemy with the word "dragon" in its name that takes up the entire other half of the screen, you'll probably breathe easy once you get used to the fact that big creatures in the game are generally fairly doable opponents. However, you'll groan whenever you encounter something tiny and cute-looking, because it's likely that the cute little "bun bit" you're fighting is going to be about three times as difficult to face as the previous so-called "behemoth".
And then we have Sally, the Supreme Necromantress of the Tower of Necromancy, in AdventureQuest Worlds. Sure, she may be a little girl, but she brought back Noxus as a lich and even helped create Hero Killer Vordred.
The Kamis from Ryzom are kinda cute, but if you do too much harvesting in one area, their magic shall fall on you like the hammer of god.
Peter the Puppy from Earthworm Jim. The levels where he appears consist solely of trying to keep him — or his puppies, in the sequel — from getting hurt so he doesn't turn into a horrifying mutant and maul Jim.
Later versions of Terraria feature bunny rabbits hopping around the landscape... which during a Blood Moon turn into Corrupt Bunnies, which can be fairly deadly foes for characters just starting out.
The 3DRealms game Shadow Warrior plays this entirely straight in a shout-out to the original. Through-out the game, you can find little rabbits running around and can even kill them without a problem. However, in one secret area, you will find a rabbit that's out for blood, complete with a discarded helmet and grail. Your character even exclaims "That's no ordinary rabbit," as the little furry menace rushes at you and begins to gnaw away your health!
In Enchanted Arms, the golem APO looks like a couple of gumdrops with small, cartoon arms and legs. No, really. It's one of the most devastatingly-effective golems in the game.
The Basilisks in Dark Souls, which look like deformed frogs with cartoonishly huge eyes. Your first thought will probably be that they look either hilariously stupid or adorable. That being said, since this is Dark Souls, they're incredibly dangerous and will slap you with the dreaded Curse status ailment, which instakills you and cuts your life bar in half until you scrounge up enough souls for a Purging Stone.
Rats! Okay, the rats in Dark Souls are disgustingly large and ugly, but come on; rats are a standard RPG mook and could never be considered a threat, right? Wrong. Prepare to get poisoned and staggered a lot.
Aww, look at the little mushroom people! They're so cute, tripping over their own feet, and they're basically harmless! Oh, here come some bigger ones! They're not quite as cute as the little-CRUNCH.
In Fable II, one of the contestants in the Crucible waiting room is Gorgoron, a cute little girl with a deep, menacing voice who claims to be a shape-shifter and master of disguise.
In Ragnarok Online, everything is cute. And higher level monsters love to occasionally hang out in lower level areas - while looking just as cute. A newbie character goes out in the field and merrily slaughters giant pink blobs, caterpillars and bunnies - but death awaits him, dare he lay a hand on a butterfly or a rare big blue bunny. A quest to become an acolyte entails a pilgrimage across a couple zones to a monastery - and those who undertake it should not attack the cute little monkeys, no matter how annoying the are, lest they will be torn to shreds by them. Later, after taking down ferocious looking wolves (and some giant violinist grasshoppers) you may think that you can take on the ladybug that stole the drops from said wolves? Nope. The list goes on.
Planescape: Torment has the Lim-lim. You can buy one on the market as a cute pet, and it doesn't do much. Then in a different area of town, you meet a circle of magicians that attempt to summon a wild one... and it promptly slaughters all of them. It's also pretty dangerous to you should you provoke it.
From the same game, both Morte the floating skull and Nordom the four-armed cube thingy are much more dangerous than they seem.
Phantasy Star has giant zombie rabbits that despite being, you know, undead, still look pretty cute with their missing ear and all, then they split in half and fire acid at you.
Galactic Civilizations has a race of evil space squirrels known as the Snathi, whose portrait is available to player empires. Some famous Let's Plays featured the "suspiciously rabbit-like" Spectres of Agony, who ate their enemies' eyeballs and ended up ascending to godhood, and their distant relatives, the Spatial Hares, who were supposed to be diplomatic and peaceful, and ended up destroying no less than 21 stars - making them the rabbits with the highest killcount on this page, measuring in the tens of billions.
Maximo vs. Army of Zin has the Rarbite, an ordinary looking rabbit that, when attacked, transforms into a vicious demon that latches onto your ankle and gradually drains your health until removed.
Any Yordle character in League of Legends would qualify for this trope, but easily the best example would have to be Teemo, a huggably adorable little chipmunk-like boy scout who will pump you full of poison darts and trap you in a minefield of toxic mushrooms. Bonus points for his Cottontail skin, making him even more of a literal killer rabbit.
Fantasy Quest offers a giant bunny rabbit that proves surprisingly lethal. The sequel kicks it up a notch with a herd of carnivorous giraffes.
Another literal example: the rabbit-people in Utawarerumono seem peaceful and diplomatic, at least compared to all the Blood Knight nations around them. People wonder how they haven't been conquered yet. Then, when they get attacked, they show it's because they still have Humongous Mecha from before the apocalypse.
In Boiling Point: Road to Hell, the helpless grannies sitting by the road are liable to start throwing grenades if you massacre civilians.
Anything from Whimseyshire in Diablo III. Cute little flowers, stuffed bears, and colourful ponies... all of which are stronger than the end-of-game enemies.
Mana Khemia has several enemies that fit this description, including Punis (jelly blobs), Koalarias (koala bears that hop around on enormous spiked logs) and Brownies (which are tiny but wield very large hammers), but the party members also have their share. Nikki's mana is a shy tree fairy with a killer Green Thumb. Pamela leaves most of the fighting to her posessed teddy and its ridiculously large claws. And then there's Muppy...
Fallout: New Vegas, the tiny deathclaw is actually a miniature version of the LEGENDARY DEATHCLAW! HP and Damage included.
Originally Zombi U was going to involve tiny evil aliens based on the Rabbids. However they were eventually changed to zombies for both gameplay reasons and a tonal shift as development went on.
Bells are Metal Slime monsters who will drop a lot of precious items if you manage to defeat them before they run away (and given that they take 5-8 turns in the time ti takes a mid-level player to take one, that is more than likely). If you manage in the even harder task of capturing one, you can give them a ranged weapon, and watch as they utterly slaughter any monster with an endless stream of arrows/bullets, and dodge pretty much everything foes throw at them. And you can experiment on them with the Gene Engineer skill to give them melee weapons as well...
The Little Girl is one of the first companions you'll get. She can wield heavy weapons like nobody's business, and evolve into the Valkyrie, a version of herself with a tiny armor and wings, and much more bruising potential.
After defeating Zeome, the Final Boss of Elona, you meet Orphe the Chaos Child, a small and innocent-looking kid...who just happens to be the Final Boss of the expansion, Elona+.
In Ginormo Sword, after expending a great amount of blood and sweat on defeating the very big and tough False God, you unlock an area where "a watchdog" reportedly resides in. So you go in there to find an adorable-looking dog/pig hybrid who's easily the tiniest out of the monsters you've encountered so far. Aww, how could this cute widdle puppy possibly be in a boss-marked arena? Then you swing your huge sword, and the puppy obliterates you with one blast of its equally huge fiery breath. Turns out its actual name is "Hellhound".
Rascal Rabbits in Seal Online are a literal example, white rabbits bearing a bloody cleaver and are carnivorous.
Max of Sam & Max: Freelance Police is a literal example. Max may not be particularly cute (though YMMV) but he is an anthropomorphic rabbit with a penchant for violence.
In Cross Edge, in certain dungeons, you have a chance to run into the cutest little pink dragon ever. This cute little dragon, Lujit, also happens to be stronger than the Big Bad, capable of the Big Bad's greatest attack - A-Fear - as well as Angelic Howl and Earthquake, and hits so unbelievably hard you'd swear someone high up has it out for you. And lets not even go into the immeasurable power wielded by its more powerful brother, Cilone.
Drakengard 3 has Zero's Flower. It doesn't do much during the various routes apart from eventually turning every Intoner into a Grotesquerie Queen, the biggest threat in the Drakengard world.