A British TV ad from the eighties about "Natural good taste" has a guy in horrible colours with yellow and purple wallpaper, who likes The Birdie Song and has a toy poodle called Rambo.
Anime and Manga
Axis Powers Hetalia has Chimamire Hana-Tamago (Bloodstained Flower-Egg), a cute, little, white doggie who gains the ability to talk during Christmas specials, in which she vehemently denies the "Chimamire" part and wishes that she had been named something nice like Charlotte.
"The Predator" from Green Lantern is The Love Entity—the living embodiment of the Violet Light that the Star Sapphire Corps uses for their powers. Despite it's name and menacing alien dragon appearance, it's actually a Big Good entity.
In Oh God, Not Again!, this trope is averted, much to Harry's dislike. In the original timeline, he and Ginny got a rabbit, and she refused to accept his name suggestion of "Mega Ultra Flame Deathsman", instead going with a more standard "Flopsy".
From Muppet Treasure Island, the infamous pirate Big Fat Ugly Bug-faced Baby-eating O'Brien, is a rather attractive looking young woman. With a really deep voice...
The "Incredibly Deadly Viper" from A Series of Unfortunate Events is totally harmless - the name was given to it as a practical joke, as it is instead playful and as cute as a sewer-pipe sized snake can be.
Hagrid's dog Fang in Harry Potter, ironically one of the only animals he tends to that isn't vicious or dangerous. Unlike, say, Fluffy or Norbert.
Lampshaded when Hagrid is splitting people up in groups to venture through the Forbidden Forest.
In Dinotopia: Journey to Chandara, the emperor of Chandara has the imposing name of Hugo Khan. Turns out that he's a Microraptor, which is one of the smallest dinosaurs known. Even the name of the dinosaur sounds puny.
In the Chalion verse, the Viking-esque prince Jokol "Skullsplitter", who it turns out was given that appellation due to his talent at poetry: he makes "heads burst with his tales". (Notliterally.)
In Louis Sachar's The Boy Who Lost His Face, Mo builds a doghouse in shop class with a sign that says Killer, hoping to get a dog to go with the house. She does, but Killer ends up being a small puppy.
According to Children of the Jedi, Leia named one of her aunt's pet pittins (kitten analogues) AT-AV (short for All-Terrain Attack Vehicle). Not hard to imagine a kitten acting like that...
In the children's book series for How to Train Your Dragon, Fishlegs has a dragon named Horrorcow. It's vaguely cow-like, but not at all horrifying.
In one of the books in Phyllis Reynolds Naylor's Alice series, a family hears that having a dog named "Killer" will deter robbers and change the name of their aged and harmless dog from "Muffin" to "Killer".
In The Savannah Reid Mysteries, subverted with Lady Eleanor's dogs, Hitler, Satan, and Killer. They're tiny little fluffy dogs, not what you'd first expect the breed to be if you'd only heard the names. They are quite aggressive at first, but once Savannah starts treating them kindly, they're rather friendly to everyone.
Dońa Clotilde from El Chavo del ocho likes to adopt puppies and baptize them as "Satan" and "Lucifer". Her poor pets also have a tendency to run off, so she tries to bring them back by calling their names loudly. Add this to the fact that her neighbors doesn't always know she has a pet, and Hilarity Ensues (she's called The Witch of Apartment 71...)
Subverted in an episode of That's So Raven which featured a Yorkshire terrier named Monster.
The GIANT DEATH RAY from That Mitchell and Webb Look. It's actually an oversized barcode scanner named after its creator, Professor Death, who is himself is something of an example: an ardent pacifist whose inventions are intended for peaceful endeavours, who happens to have the surname Death.
In Season 4 of Buffy the Vampire Slayer, the gang is plagued by Gachnar, a fear demon. Buffy is overzealous and breaks his giant symbol, freeing him to the revelation that he was only a couple of inches tall. After some cooing, Gachnar then gets squashed by the slayer's boot.
Giles: Don't taunt the Fear Demon. Xander: Why? Can it hurt me? Giles: No, it's just tacky.
Same joke, way different execution occurred in Angel when Cordelia, as a princess, and to her vocal disgust, is coerced to mate with a hideous, destructive monster called the Groosalugg...until she finds out 'Groo' is only hideous by demon standards; he's actually an incredibly handsome and skilled human warrior and really quite sweet in temperament. (She still doesn't mate with him, but for different reasons.)
In a live action skit spoofing God of War, X-Play had Kratos's final opponent be the God of Chaos, which happened to be a cute little puppy.
The Fallout games have a faction known as the Followers of The Apocalypse. With a name like that, you'd expect them to be really evil or at least really metal. Instead, they're probably the setting's most altruistic and harmless factions, being essentially the post-apocalyptic Red Cross. The name stands for the fact that they seek knowledge of the Old World so that mistakes like the Great War can never be repeated again. Of course, one of their former members happens to be the founder of Caesar's Legion, though he's considered the Black Sheep of the faction.
In Fallout: New Vegas, there's a Super Mutant by the name of Mean Sonofabitch. He protects the slums of Westside from raiders and is a Gentle Giant at nature (though somewhat unintelligible due to having his tongue cut out by some Sociopathic Soldiers).
Used to hilarious effect in Mercenaries 2. There's a mission that tells you to get something called the Devastator. At first, the pointer seems to lead you to a gigantic tank...but then, after you get in, the pointer shows the Devastator is a cute little scooter.
Captain Dread of Monkey Island 2: LeChuck's Revenge. Remember that "dread" is a word with more than one meaning. Bonus points for being the only Jamaican in the series so far.
Pokémon's nickname function lets you have this, Fluffies, and Deathbringers that grow into their name when they evolve.
There is also Gorebyss, which immediately bring to mind "an abyss of gore," unless you know what it looks like. In all fairness though, it is "gorgeous," and does live in an "abyss", as in "the bottom of the sea". However, that's just a facade. Its actually very aggressive and hunts by Mind Raping its prey, shoving its extremely sharp mouth into their unconscious bodies, and sucking their fluids out. Yes its beautiful, but the name fits.
Paarthurnax in Skyrim. Admittedly, he is a dragon, but for someone who's name means "Ambition Overlord Cruelty", he's really nice. As in, Actual Pacifist levels of nice.
In the old days he really did live up to his name, being The Dragon to the Big Bad. His current state is a self-imposed penance.
In Jagged Alliance 2, there is a character named Spider. She is a kindly, maternal medic and absolute pants at everything killing-related. She got the nickname from her brothers, who teased her about her fear of bugs. Of course, thanks to her high wisdom stats, she gets better at everything killing-related scarily fast. Which the developers fully intended and added lots of Break the Cutie moments into her dialogue. Statements like: "How can anyone see that and not question what we do for a living?" are only the beginning.
In Super Dangan Ronpa 2, Gundam Tanaka has a group of four hamsters he named "The Four Dark Deva Lords of Destruction". Of course, they're not completely harmless, as one of his hamsters makes him possible to kill Nekomaru Nidai by sneaking and pressing a button to shut Nidai off until he ties Nidai up in a place where a struggle will get him killed.
In the Housepets! universe, wolves traditionally name themselves. Babylon Garden's resident wolf has half-a-dozen kids who can't wait to name themselves. Among current suggestions are "Deathaxe" and "Space Laser".
Miles: ...We try to put this off as long as possible.
This trope is named after DMFA 's "Deathbringer", an incredibly cute bubble-gum creature. While she picked out her own name, she has so far demonstrated absolutely no aggression nor offensive capabilities whatsoever. The four characters that know she exists also call her Deebs for short.
Casey and Andy has the PLANET DEVOURER! However, it does eat Mars. A model of Mars, not the actual planet. Later on, it proves able to chew through Satan's most powerful magical artifact. The Planet Devourer actually can devour anything... it just has to do so one dainty nibble at a time.
PvP features an adorable kitty cat named Scratch Fury, Destroyer of Worlds. It could be called subverted—Scratch actually wants to conquer the Earth—but he's so easily distracted by cat things that he's ultimately (mostly) harmless.
Flintlocke vs. The Horde has Bun'kar, the warrior bunny. Being a hunter's pet, it might become Killer Rabbit later, though. While Bun'kar, the warrior bunny, never fights, he and his hunter manage to overpower at least three characters, one of which was significantly stronger. The healer(Doc) remarks "That rabbit was dynamite."
"Please do not nuzzle the instrument of my vengeance."
When 8-Bit Theater's Light Warriors had Drizzl surrounded and down for the count, Drizzl attempted to summon the "True Guardian" of the cave, which he had bought from Con Man Akbar based on its description as a fierce chimera with claws, fire breath, and potent venom. Drizzl discovers at the worst possible moment that the creature was just a platypus with a makeshift flamethrower strapped to its underbelly.
In Mokepon, Elle uses a Diglett named "Gutripper".
Usagi-Kaiju is a very realistic stuffed animal rabbit but, as she a mostly called, another name for her would be Deathbringer.
My Life as a Teenage Robot has Killgore. Name that sounds like something that would rain destruction, but actually just a cute little wind-up toy who insists he's unstoppably evil.
Planet Sheen: Boh-Rok, a rainbow-colored pony, was thought to be a destructive monster. Sheen manages to remove a nose hair that was bothering Boh-Rok and it turns out that he isn't as evil as the aliens thought, but rather, a cheerful, happy pony.
Ruby Gloom has the Doom Kitty, an otherwise normal, if intelligent and expressive, black cat.
Chainsaw from Goof Troop. Despite her dangerous name, she's a mostly harmless cat-sized lapdog with a bow. The worst thing she ever does is chase the neighbors' cat.
The title characters from The Chubb Chubbs.
The Great Shrike-Tyrant. Sounds like some sort of Lovecraftian shark, right? Nope — it's a cute little bird. The whole genus is called 'tyrannus' because they aggressively chase other birds out of their territories.
Actual shrikes are also cute little birds whose Latin name means "butcher," and they're often called "butcher birds." Why? Because they impale their prey on thorns. It sounds nastier than it is. They're really just saving bugs for later.
Bloodhounds are among the gentler dog breeds. They actually got their names because they are hunting dogs with the main purpose of following blood trails.
The death's head hawk moth, which has a badass name not only in English but in Latin as well. Acherontia atropos (which does geniunely sound omnious if you know your Greek Mythology) has also a skull motif on his back. But yet it's a butterfly, and it can't even hurt anything. Despite its Real Life reputation as a harbinger of death and evil. All that it does which is harmful that is raiding beehives for honey.
The ominously named Purgatorius was a small mammal that was one of the first species to emerge after the death of the dinosaurs, and the ancestor of the primates.
Due to the company's Goth aesthetic, many of Black Phoenix Alchemy Lab's perfumes have ominous names, although few of them smell particularly menacing. For instance, Shub-Niggurath smells like incense and gingerbread, and Al-Shairan has the demonic reek of spiced oranges with a hint of peach.
The tiny and adorable pygmy marmosets at Edinburgh Zoo are named 'Terminator' and 'She-Ra'.
The Slavic name "Dragomir," to English speakers. Despite sounding like it means something about dragons or devils, it actually means "He who loves peace." Whether individual Dragomirs (Dragomiri?) are this, Fluffies, or anywhere in between is up to them, obviously.
The caterpillar of moth species Citheronia regalis is so-named hickory horneddevils because of their spikes, but unlike most spiky/fuzzy caterpillars, these 'devils' ' spikes are not that dangerous to humans (as in, not loaded with venom etc). Plus, they grow up into moths, which are usually not nasty insects (although regalis moths are relatively large insects).