BioShock 1 makes strong use of this trope. Splicers wear bloodied bunny masks. The mad artist Sander Cohen is fixated with rabbits, using rabbit masks in his tableaux and rabbits in his... poetry.
"I want to cut the ears off, but I can't...I FUCKING CAN'T!!!"
Bravely Second has an early rabbit enemy that looks cute and fuzzy at first. However, when it attacks, it has a mouth that opens much too widely, and More Teeth than the Osmond Family. The characters even discuss this on the creature's bestiary page.
The titular bunnies from the flash game series Bunny Invasion are laboratory mutants from an outbreak that, while not looking menacing or different from typical rabbits for most types, are extremely violent and seek to kill all people around them. In each of the three games in the series, the protagonist Mr. Frost defends a different building from them (his house in the first game, a pub in Bunny Invasion 2 and a motel in Bunny Invasion: Easter Special).
There are rabbit monsters in Catacomb Armageddon that look like harmless bunnies hopping on the spot (yes, that's rather weird) but turn into large semi-humanoid monsters to attack.
The Mimiga from Cave Story are a group of peaceful and friendly rabbit-like creatures...unless you feed them Red Flowers, which turns them into mindless rampaging beasts. They're fully aware of this, which is why they don't grow red flowers in their village.
T-Hoppy from the ClayFighter series is a musclebound rabbit with a machine gun for an arm. He seems to be the most verbally abusive character in a game full of verbally abusive characters.
The Huntress is a Crazy Survivalist who had a modus operandi of killing families before "adopting" any daughters they had, who would subsequently die due to neglect, and who currently serves a God of Evil and provides it with human sacrifices. She additionally wears a mask styled after a rabbit's head.
The Animatronic, Springtrap of Five Nights at Freddy's fame, is a Guest Fighter. Like in his home series, he is a rabbit animatronic possessed by the restless spirit of a child murderer, who eagerly accepted the Entity offering him a job as one of its Killers so he could kill to his heart's content.
In Demon Front, Sarah's Attack Animal is a rabbit-like alien named "Bunny" who can launch exploding bubbles capable of dealing severe damage to vehicles and killing plenty of mooks. It's also invincible, to boot.
Dragon Quest X has the Robber Rabbit monster family, which are bunnies that wear Thug Masks who made a living by pilfering crops from farms and perform nasty Drop Kicks on their enemies. Their stronger Ripped Rabbit, Rottontail, and Bad Hare relatives are no slouches either, with Ripped Rabbits and Rottontails using Double Up, which increases their ATK while sacrificing their DEF, and Multifists, which is also used by Bad Hares in battle. In addition, Bad Hares themselves have Flying Footwallop, a stronger version of Drop Kick.
Dragon Quest XI features the return of the Robber Rabbits, Rottontails, and Bad Hares, though the Ripped Rabbits are Put on a Bus for this main series entry. In addition to the 3 aforementioned monsters fighting the same way as in the previous game, Bad Hares now have a Pep Power named Ballistic Kick, which combines their Flying Footwallops to damage 1 enemy while potentially making them fall.
Dunkadillo: The first boss, Hitter Critter, is a giant rabbit with red eyes who tries to squash the player character with its paw.
Members of the virtually extinct Taguel race in Fire Emblem: Awakening (like Panne, her son Yarne, and potentially a Morgan parented by either of them with the Avatar) are capable of transforming into sleek rabbit beasts with some wolf-like characteristics. They're talented at taking down ground cavalry, and focus more on speed and skill then their fellow shapeshifters, the Manaketes.
Final Fantasy XII has dreamhares, which are less Killer Rabbit and more Goddamn Bats thanks to being Fragile Speedsters with a focus on buffs and debuffs over damage-dealing. Most of the generic ones you encounter are docile and will not attack unless provoked (they may even heal you if you stand nearby), aside from the Mus from Feywood, which happily spam Confuses the instant they see your party. Their king is Fury, a cute purple dreamhare who lives in the grim and creepy Necrohol of Nabudis, and its debut comes when you think you're about to fight a scary-looking Catoblepas, only for Fury to appear out of nowhere and one-shot it. The game actually includes an enemy that is called Vorpal Bunny, but it just takes the genus' "bat" status up another notch.
Final Fantasy Tactics A2 features the return of dreamhares. It also has the Mooglebane, which is known for devouring Moogles' pom-poms, one of their worst nightmares. The monster's skill set is even renamed "Pom-pom Puree," though it really doesn't gain any mechanical benefits from its comically monstrous reputation.
Five Nights at Freddy's 1 starts out with Bonnie, the first animatronic to harass the night guard and contains the spirit of a murdered, vengeful child inside.
Five Nights at Freddy's 2 introduces Toy Bonnie, an animatronic straight out of the Uncanny Valley, and Withered Bonnie, an older version of Bonnie missing its upper jaw and will eventually be repaired to become FNAF 1's Bonnie. There's also the mysterious RWQFSFASXC, aka Shadow Bonnie, whom if stared at too long crashes the game.
Five Nights at Freddy's 3 introduces the most sinister example of this trope for the first time, Springtrap, a decayed animatronic initially created to be versatile enough for humans to wear. It contains the corpse of the Big Bad of the series, William Afton, who's responsible for all the child murders.
Five Nights at Freddy's 4 has Nightmare Bonnie, a literal nightmare version of Bonnie with More Teeth than the Osmond Family. The Halloween DLC also brought in Jack-O-Bonnie, a version of Nightmare Bonnie who glows as if on fire, and Plushtrap, a miniature version of Springtrap that still can kill if it gets too close.
In Freddy Fazbear's Pizzeria Simulator Springtrap returns as Scraptrap to terrorize more kids. Double Subverted with Rockstar Bonnie, though: while he was initially an aversion, only being used to entertain the pizzeria, Ultimate Custom Night changes that and he becomes a genuine threat to the player (and actually has a reputation as a huge 50/20 run killer due to his game mechanics).
Five Nights at Freddy's VR: Help Wanted introduces the mysterious Glitchtrap, a bunny mascot (notably not an animatronic) that periodically waves at the player during the VR simulator. Either William Afton's soul somehow got into the game and he's trying to use the protagonist to escape, or the Mimic has taken on a form similar to him to serve as a copycat killer.
Five Nights at Freddy's: Security Breach, notably, does not have a Bonnie in it (it's explicitly stated management is trying to Un-person him), but still has an example in Vanny, a person in a white bunny suit who reprogrammed the normally benevolent animatronics into becoming killers to attack Gregory. Her real identity is Vanessa, the protagonist of Help Wanted, under the influence of Glitchtrap to restart the child murders and resurrect him as Burntrap, a heavily decayed version of Springtrap that demonstrates a new ability: the ability to control the animatronics.
Security Breach's Ruin DLC finally proves that Glamrock Bonnie was an aversion as he was broken apart (by who is implied to be Monty) and left for dead before the main game even began. The DLC also introduces a downplayed example in M.X.E.S, a security AI shaped like a purple rabbit who can't actually kill Cassie itself, but can call for animatronics that can kill her. Then The Ending Changes Everything: M.X.E.S. had very good reason to do what he did, as his role is to keep the Mimic sealed away, and Cassie was inadvertently releasing him with her actions.
Five Nights at Freddy's: Help Wanted 2, along with the returning examples of Bonnet and Bon Bon, have who is implied to be Glitchtrap interfere with monitors in the various mini games. If the player activates the Princess Quest game, the enemies the player fights are giant floating rabbit heads. The Secret Ending also sees Glitchtrap and Vanny return....except since Ruin implies the Princess Quest ending of Security Breach (where Vanessa's brainwashing is broken and she Heel Face Turns) is the canon one, Vanny is now an aversion and crushes Glitchtrap in her hands.
A partial example in Five Nights at Freddy's: Secret of the Mimic: one of the bosses of the True Ending of the game is M2RND, a horrific amalgamation of the future FNAF 1 animatronics possessed by the Mimic. The head, at the least, came from Bonnie.
Jack Holmes : Master of Puppets: Among the animatronics in the park, there's one of a human-sized rabbit that seems to be inactive... only it moves when Jack's not looking at it. Spend too long around it and the rabbit animatronic comes to life and stalks Jack.
This trope is whole point of Jazz Jackrabbit. It doesn't matter if you are a small rabbit as long you have a BFG.
In Jedi Knight: Dark Forces II, if you perform certain actions you can unleash Max from Sam & Max on a level. He will move through the level, murdering any enemies unfortunate enough to cross his path.
From Kingdom Hearts: Birth by Sleep, we have a type of enemy called the Hareraiser. Small, cuddly, and seemingly harmless. It shows up in one of the first levels avaliable to you when you play as Aqua, and are teeny-tiny compared to other early enemies. However, these things can attack multiple times with one move, do a lot of damage with every hit, and kill you before you can finish going "D'aww". Worse, they typically appear in packs of four or more. And there is usually more than one pack in a given location.
The nightmare versions of the Me Me Bunny and Majik Lapin in Kingdom Hearts 3D [Dream Drop Distance] qualify, with their creepy red eyes and unpleasant coloration. They also have an annoying tendency to become completely immune to physical attacks, which turns them into definitive Goddamned Bats.
The primary enemy type you run into in The Long Drive are large rabbits that nearly come up to your character's waist, which let out horrific shrieks when they see you before trying to maul you to death. While they're a major example of Artificial Stupidity to the point they're more likely to accidentally kill themselves instead of you, potentially lessening their threatening image, the shrieking is still very unnerving to hear come out of nowhere at night.
Monster Hunter Portable 3rd instroduces Lagombi, a fifteen-foot-long giant snow hare with an armored torso and an unpleasant temper.
In Murder House, The Easter Ripper is a serial killer who pursues his victims clad in an Easter Bunny costume.
Mr. Hopp's Playhouse: Mr. Hopp is a demonic stuffed rabbit hellbent on getting you.
Night of the Living Robot: The Pumpkin Rabbit is a huge animatronic bunny with a creepy grin and too-small eyes. He's also the only antagonist to appear in all of the minigames.
Overgrowth has you playing an anthropomorphic rabbit who can dispatch dozens of his furry fellows with some bone-breaking martial arts. Things only get more decisive when weapons like swords and spears get involved.
In Persona Q: Shadow of the Labyrinth, Rei's Shadow Self, Best Friend, takes the form of a giant stuffed rabbit. When the Shadow transforms into Best Friend, the stuffings inside the rabbit doll that she holds engulfs and fuses her into the monstrous rabbit plush toy.
In Persona Q2: New Cinema Labyrinth, after you beat Kamoshidaman, the Designated Hero of the first movie, he uses a pair of carrots to transform into his One-Winged Angel form, a monstrous wererabbit with Kamoshida's face on it, holding a pair of carrots as BFGs. While the transformation might seem sudden and unexplainable, the late-game does provide a clear reason that descends into horrifying implications: The rabbit form is supposed to represent the class pet in Hikari's primary school, a rabbit that was poisoned by some spoiled food and died. In reality, her teacher (Who is the base for Kamoshidaman) gave the students spoiled food to feed the rabbit, so she probably didn't even care for it. Hikari only warned the students that the food was spoiled but nobody heeded her, and the teacher scapegoated and humiliated her in front of the class because she didn't apologize for something she didn't do.
Phantasy Star II features zombie rabbits that are constantly scooping their intestines back into their chest cavities and would attack you with them.
In Pity Party, the rabbit-headed guest isn't exactly cute and cuddly. He snaps at you for not having "toppings" ready for the cake or carrot, and it's soon discovered he's hiding a big knife in his jacket.
The Lepus Marihares in Planet Explorers have a fluffy, rabbity look. They are also fearsome predators which will gladly go after humans. (They're by no means the strongest enemies in the game, though.)
One of the main enemies in Ben "Yahtzee" Croshaw's Poacher are carnivorous rabbits, including giant ones called bargests.
The Pokémon franchise has a few rabbit-like Pokémon. Most of them are mid-to-low strength Pokémon that don't really stand out from the pack though.
Gen I introduced Wigglytuff, the vaguely rabbit-like evolved form of Jigglypuff.
Gen I also introduces the player to both gender variants of Nidoran. Both are cutesy rabbit-like Pokémon who happen to have sharp and very poisonous spines and horns. Their evolved forms (Nidorino and Nidorina) look more ferocious and dinosaur-like rather than the cutesy bunnies they started out as. And, using a Moon Stone on either will cause them to evolve into their final forms, which are essentially expies ofBaragon.
Gen II introduced Azumarill, the "Aqua Rabbit Pokémon" which evolves from Marill. It can play the trope straight thanks to the ability Huge Power, allowing it to rip apart enemy teams with ease with Aqua Jet, Waterfall and Play Rough.
If Eeveelutions are being considered, two most rabbit-like Eeveelutions have the most-fearsome reputations:
Umbreon has some of the dangerous reputation in some of its Pokédex entries. Being a Dark-type, it is a vicious predator who hunts down prey via stealth.
Sylveon has the airy and pastel appearance with its ribbon-like feelers, but being a Fairy-type and all, it has The Fair Folk aspects being played up in certain situations. The feelers are reportedly used for it to lure its prey before hunting them down in a predatory way.
Gen III introduced Whismur, though it loses its rabbit-like appearance as it evolves.
Gen IV introduced Buneary and Lopunny, the "Rabbit Pokémon". Lopunny then gained a mega evolution that makes it become part fighting and it gains the Scrappy ability, which lets it hit ghosts. It's even described that it undergoes a personality change from mild-mannered to highly aggressive.
The lore mentions that Buneary can shatter boulders with their ears. Getting into the mechanical side of things, Buneary is the only Pokémon that can learn the move Frustration and the only non-legendary Pokémon that starts with a friendship level of zero—by implication, they start out trusting nothing and use their paranoia to fuel a powerful attack.
Gen VI introduced Bunnelby and Diggersby who also play this straight as they have Huge Power as their hidden ability, allowing Diggersby to dish out some of the most painful Earthquakes in the game.
Subject 3 from Professor Layton and the Unwound Future. He's a former lab animal who, after years of being subjected to horrific experiments, has a rather dim view of humanity. Like everyone else in the Layton-verse, however, he's willing to forget about his threats to rearrange your kneecaps and let you pass if you solve a puzzle first.
The meat-grinder bunny-monsters in the final stage of Psychonauts.
Zig-zagged in Quest of Yipe, a trilogy of Macintosh RPGs. The rabbits in the game are all enemies, but they are The Goomba.
The titular characters of the Raving Rabbids series were introduced as evil and violent rabbit-like creatures who wreak havoc while screaming unintelligible gibberish. Nowadays they're not so much evil as they are just Chaotic Stupid. Mario + Rabbids Kingdom Battle even has a few Rabbids who are outright heroic.
Rotund Rebound is an indie game where you play an absolutely badass rabbit who goes around the woods beating up assorted animals, ending with it's Final Boss being a huge (and purple, for some reason) rabbit kaiju. It's a Background Boss that's so huge you can't see it's entire body the entire battle while it tries slapping you with it's paws.
The rabbit-imps in Rule of Rose are no less creepy than the standard variety.
Robbie the Rabbit from the Silent Hill games. He's an even more jarring example because he is nothing more than a pink stuffed rabbit (with a red stain on his mouth, sure)... that doesn't do anything. Except point at you.
He also appears as a representative of the Silent Hill series in the mobile phone version of Konami Krazy Racers. Aside from removing the red stain, no attempts were made to reduce his creepiness.
The Social Bunny in The Sims 2. If your sim's social meter goes low enough, an imaginary friend comes along to help... an imaginary friend in a stained, worn, creepy-looking bunny costume that is missing an eye. Eeeeugh.
In Tails' Skypatrol, the boss of MetalIsland Area is Carrotia, a rabbit who works for Witchcart. She rides a carrot-shaped plane, and attacks Tails by firing carrots as missiles and blowing kisses.
Bunny from Sonic 3D Blast is a robotic rabbit who inhabits Diamond Dust Zone. He rides a pogo stick and hops in an erratic motion around a set point, only harming Sonic if the hedgehog bumps directly into him.
Peppy Hare in the Star Fox franchise downplays and inverts this trope, being one of Fox's staunch allies and the advisor of the titular team. The reason why he's a downplayed inversion instead of a straight-up inversion? As a member of the team, Peppy's no exception to the rule of the team shooting enemies down, scoring his own fair share of kills.
Mega Man 2 has the Robbit enemy that appears in Wood Man's stage. It hops forward and fires carrot-shaped missiles at Mega Man. They reappear in Mega Man 11 in Tundra Man's and Torch Man's levels, though they lack the ability to fire missiles.
Mega Man X1 has the Ray Bit enemies in Chill Penguin's stage. They have blasters built into their ears and will try to hop into X.
Super Mario Odyssey features the Broodals, a band of sinister anthropomorphic rabbits who serve as both Bowser's wedding planners and the game's Quirky Miniboss Squad. Their leader, Madame Broode, is equally sinister, helped in no small part by her pet Chain Chomp, Chain Chompikins.
The game has cute little bunnies that wander around the landscape and frequently get killed by enemy slimes or inadvertent player actions. However, during the Blood Moon, they transform into vicious purple Corrupt Bunnies (or Crimtane Bunnies in Crimson worlds) with glowing red eyes. Only the Corrupt version drops a wearable bunny hood as loot.
In the mobile version, you fight Diseaster Bunnies on Easter. They're just as dangerous as Corrupt Bunnies, and they may drop a Suspicious Looking Egg. If that is used, it summons Lepus, a huge rabbit boss that lays eggs that spawn more Diseaster Bunnies or a weaker version of itself.
Fluffy Fluffy Bun Bun from Toonstruck. She pretends to be a cute, innocent bunny throughout Disk 1, but it's revealed at the end of Disk 1 that she was Evil All Along. She forms half of the Big Bad Ensemble with Count Nefarious, and like him, she is a megalomaniac who wants to take over the world.
Touhou Project Reisen Udongein Inaba, when she's using her madness-inducing power.
Tewi Inaba becomes a little frightening if you read the supplemental material and think about it for a while. Among other things, it's implied that being in her good grace is the only reason the moon fugitives can stay at Eientei, and that she's far more powerful than she lets on.
The Black Rabite from Trials of Mana. Rabites are mostly harmless, even though they can have levels in SD3 and can occasionally outclass you, but the Black Rabite is the hardest boss in the game. You will never feel safe around a legless rabbit again.
An Easter Egg Hunt themed Warcraft III map has seriously horrifying bunnies.
One of the contestants in the video game Whacked! is an amputee rabbit named Lucky who has quite the violent temper.
World of Warcraft introduced the Darkmoon Rabbit, an obvious homage to Monty Python and the Holy Grail. It latches onto and chews through the necks of players and has enough health that it requires a large raid to be killed. Visually, it is notable for being white with red bloodstains on its muzzle.
In the Mists of Pandaria expansion, we get the Virmen, a race of anthropomorphic rabbits that straddles the line between this and Rascally Rabbit. They're mostly found in the Valley of Four Winds as a farm pest.
that are constantly scooping their intestines back into their chest cavities and would attack you with them.