From Fullmetal Alchemist, Pride. Aww, look at the cute little boy. Say, why are the shadows moving towards me and why do they have eyes and sharp teeth? Wait... ARGH!
Road Kamelot in D.Gray-Man certainly qualifies. She looks no more than twelve - yet in one of her first appearances she stabs the main character's eye with a candle, then licks the blood off afterwards.
Doubt - if you read later on... Grotesque cuteness indeed.
The main School Days series was already infamous for its bloody finale... And then comes the Magical Heart Kokoro-chan OVA, with the eponymous loli helping pilot a giant Hello Kitty, chainsaw-wieldingCombining Mecha, ripping apart the enemy and drowning the city in a sea of blood. Yeah...
The same scene in the manga version is even worse.
Shizuku from Hunter × Hunter embodies this trope, being essentially a childish collection of moe tropes who happens to be a member of the most bloodthirsty group of criminals on the plannet.
Her first appearance has her acting completely moe and scatterbrained, losing a round of arm wrestling to Gon because she forgot that she's left handed. Her second appearance has her smashing two named characters' heads into paste with a completely stoic expression.
Pandora Hearts. EVERYONE works with this trope, but the ultimate would have to be Lily. She's an adorable little girl....who has a demonic dog who can and will rip your throat out. And that's ignoring the fact that she made THIS FACE.
The Littlest Cancer Patient with mutated hands and teeth fit for tearing through raw meat was making low, growly sounds. She was also poking at her dairy products in dainty, neat motions. It was kind of adorable... in a freakish, disgusting way. Was there a word for that? Grotesque cute? Ugdorable?
There's a certain element of this to V in V for Vendetta. Round, pink cheeks; Eyes Always Shut; huge smile; little upturned nose (at least in the comics); silky, shoulder-length hair... and he kills people with his bare hands!
In Dean Koontz' book, Brother Odd, the title character encounters a manufactured animal who is the epitome of mindless cuteness. Mindless, in that it has no mind or soul and is therefore profoundly disturbing rather than cute.
The suicidally depressed giant teddy bear in the Supernatural episode "Wishful Thinking".
The Criminal Minds episode "Uncanny Valley" was aiming for this as a general feel. It was an episode where the Unsub, who had her dolls taken away from her by her father kidnapped humans to serve as her dolls. It came complete with very kid-friendly music throughout.
Invoked in the music video for "Bloodline" by Slayer, where a kitten can briefly be seen lapping up a pool of blood.
Too many Rin and/or Len songs to count. A few examples? Any Evillous video where they play an incarnation of Hansel or Gretel, Trick and Treat, Karakuri Burst....et cetera.
Vampire: The Masquerade's vampires keep the looks (and age) they had at a moment of their death and vampiric transformation. So, it's possible to meet (or play as) a hundreds of years old undead monster, who looks like an angel-faced 10 years old.
Pushed Up to Eleven in the old (and VERY disturbing) Montreal sourcebook (made by White Wolf's "Black Dog" imprint, which in itself should be considered a warning), where not only is there an angel-faced 10-year-old vampire -who's her pack's warrior- but the local vamps' unofficial mascot is a limbless dwarf Samedi (vampires who look like rotting corpses) who they use in a variety of gory "games", like "bob the apple" but with humans stuck up to their necks in a flour silo. No points for guessing the place is a Sabbat stronghold.
Pathfinder goblins can fall into this, when their funny little songs and childish antics crash hard against their general violence and destructiveness.
Robbie the Rabbit, the mascot of the Silent Hill Amusement Park is a pink bunny wearing a blue overall whose most prominent feature is the blood-stained mess on his mouth and clothes. Heather from the third game says that "it is more creepy than it is cute". Coming from a girl who has deadpan snarked her way through the eponymous town, without batting an eye to the overall gory insanity around her, this says a lot.
Dahlia Hawthorne in Phoenix Wright: Trials and Tribulations is extremely cute and beautiful, even with pure white butterflies flitting about her. However, at the end of the first trial, after she's been accused of murder, she actually incinerates her butterflies with pure rage.
The Creeper from Advance Wars: Days of Ruin. Flowers are pretty. Which makes a bio-weapon that makes flowers sprout from underneath and fatally turn you into a floral display in a most painful manner all the more disturbing.
She wrenches open the lid of a nearby sarcophagus, and countless articles of stationery, toiletries, and household goods with her face on them pour out. My god, she's everywhere! Aargh!
In the Kingdom of Loathing universe, seals aren't adorable fuzzy flopping creatures as in real life; they're hideous, shambling, bloodsucking monstrosities that happen to look like adorable fuzzy flopping creatures, one of which looks more like a mutated leech than any land mammal. That said, one familiar you can acquire as a Seal Clubber is an Adorable Seal Larva, which intersperses descriptions of it sucking the blood from your opponent and bursting into an enemy's corpse so it can regurgitate a healing fluid into your body with gushing about how adorable the thing is.
Considering how cartoony the characters in the Metal Slug series are, some of them die in fairly bloody ways.
Messiah has the contrast between Bob, a sweet, chubby cherub who looks like a winged baby in a diaper, and the violence and brutality throughout the game (a lot of it inflicted by Bob himself.)
Charby the Vampirate is described as an ultra-violent Saturday morning cartoon, with adorable characters who will occasionally eviscerate or suffocate their many victims, brutally, with no Gory Discretion Shot. The combo is especially obvious with Mye, the zombie girl who smells sweet despite 315 years of decay, plus the unhealed slit in her chest where she got a sweet heart transplant. Her Evil Eyes are bubblegum pink.
Mye isn't decaying,(she is a traditional zombie, not a Hollywood/Romero zombie)the sweet smell is candle wax and gummy bears, two things she spends a lot of time with. And her brother's eyes are pink, too!
The Unspeakable Vault (of Doom) is a Lighter and Softer look at the Cthulhu Mythos—for instance, its cartoonishly-drawn "Cthulhoo" says "yum yum" every time he eats an unfortunate cultist. But it's still the Cthulhu Mythos, and the gore factor actually goes up compared to Lovecraft's work. It'd be Mood Whiplash if the death and dismemberment weren't so heavily integrated into the comic alongside the silliness.
The other Trolls do as well, albeit to a lesser extent. This seems to be a fact of which they are both aware and proud, given that they decide to call themselves "Team Adorabloodthirsty."
Homestuck in general qualifies. It starts off simply being about a kid who is celebrating his thirteenth birthday by playing a new game. Then the game turns out to cause The End of the World as We Know It and summon monsters wearing jester hats to torment the protagonist, and it only gets worse from there on out. It becomes more clear later on, with Jack Noir slaughtering an army, a children's show's characters turning out to be representations of "horror terrors" and comic relief character Gamzee going Ax-Crazy and deciding he needs to kill all his friends.
The diaries of Vriska's ancestornote A distinction granted near-legendary status since troll reproduction precludes the notion of actually knowing who your direct ancestors even are suggest that this is not only normal, but expected and encouraged of trolls of Gamzee's rank; in troll society, such traits are considered the mark of strong leadership skills.
Also, Caliborn. One of the first things we see him do after his proper revel is gnawing off his leg, causing him to get covered in his own blood. As for his personality, he's a sociopath of a Jerk Ass that seems to find the sight of his "sister's" friends dying/being knocked out hilarious. All that being said and done, he still has large, rather adorable eyesnote Plus the eyelashes, and as a cherub, he's the pinnacle of Ugly Cute.
In an attempt to tone down the violence and make the strip more viewer friendly (or so we are told), Kagerou brings us "cute chibi blood".
The Order of the Stick: The stick figure art makes everything look much cuter than it would in a more realistic style. And yet you still get characters like Xykon and Belkar and quite a bit of violence. In particular, Tsukiko sleeps with an adorable Xykon plushie, and Belkar is a fuzzy-footed halfling of chibi proportions who gleefully stabs everyone who crosses him or has something he wants.
Sonichu unintentionally falls into this. It looks a lot like something your seven year old child would draw, with creatures that are a combination of Sonic the Hedgehog and Pokémon, with an Author Avatar that is the mayor of the town and cartoon-y villains. However, it features graphic sex scenes and true to this trope, scenes where a bunch of Internet trolls are tortured to death, including one getting drilled in the groin by a little girl.
Ruby Quest is more or less about taking some cute animal people and then breaking them physically and mentally in horrible, horrible ways.
The Grim Adventures of Billy & Mandy once had an episode entitled "Wishbones" in which a skull granted people's wishes, with results of varying degrees of misfortune. Pud'n's wish was that he had a little talking bunny that always loved him. Although the bunny wasn't THAT cute, it proceeded to chase Pud'n around, beating him and trying to murder him multiple times, ending with HALF OF HIS FACE BLOWN OFF OF HIS HEAD IN DETAIL WITH THE WORDS "Sometimes love hurts, Pud'n, and I love you....to deeeaaaattthhh...." as he hopped towards Pud'n slowly. Oh, and this is a children's show.