Sam & Max: Freelance Police: The eponymous duo, especially Max. Max varies from being cute to psychotic at the drop of a hat. Sam is more reserved but can be aggressive if the time is right. And both can (and will) shoot people if they mess with them.
Runaways: Molly Hayes. A cute hat, a giant's strength.
A group of Marvel staff ("The Secret Cabal") couldn't put her on their list of "Top Ten Teen Heroes" because she technically isn't a teenager yet, but they stuck her on the list anyway. The picture they put on the list for her Moment of Awesome: Gut-punching the Punisher. She's eleven years old, goes by the moniker "Princess Powerful," thinks it's important that every burglar wear stockings during a crime (even if they do give her "waffle-face") and she's punching the Punisher. Yes, that Punisher. It's worth noting that Molly felt terrible about the incident with the Punisher afterwards, since she had assumed the the Punisher had actual powers and could take the hit. This of course, only makes it more adorable.
Molly did the exact same thing to Wolverine, only hard enough to send him flying about fifty yards.
Piffany of Nodwick. Cleric of fluffy sweetness who draws duckies and bunnies when the Gambit Pileup she's been diagramming gets too complicated, yet greater demons are TERRIFIED of her.
Gully from Battle Chasers. Not yet nine and half, blonde, green eyed, utterly cute - and wields the Gloves of Aramas which give the wielder the strength of a thousand men. With them, she pwns a pack of werewolves (inadvertently beating one of them to death) and stops a demon at least ten times her size in its tracks long enough for her companion war golem to destroy the containment bracelet, sending it back to Hell permanently.
Amy Rose, wielder of the Piko Piko hammer, is also hyperactive, and adorably in love with the protagonist, Sonic.
And then there's Cream, while an Actual Pacifist, will get really angry and stare down bullies. When she flipped out over how Team Hooligan (Nack the Weasel, Bean the Dynamite and Bark the Polar Bear) were making their search for the Sol Emerald even tougher, even they had to recoil back in shock.
Lord Noriyuki in Usagi Yojimbo. He rarely has to fight personally (his soldiers do it for him, plus he's about 10-11 years old), but he's good at throwing knives.
Galacta, the daughter of Galactus. An adorable Meganekko young woman who goes by "Galli" who happens to be the daughter of one of the most powerful beings in the Marvel Universe — and she is almost as powerful as him.
Power Pack, especially the modern mangaesque version, has Energizer, a 6 girl who is the team's firepower and cute as a button.
Miho from Sin City. She's very small and cute but will decapitate you at the drop of a hat.
Shazam: Captain Marvel from DC Comics. As someone who is really just an adorable kid (between 12 and 16 years old depending on the writer), and the epitome of 'nice guy' in the DCU (even moreso than Superman), he often comes off as a very sweet, kind hero who is easily flustered when women show interest in him or when he does things like befriending sick children at a hospital in "Power of Hope". Despite that, he will take on any opposition, up to and including DC's version of Satan and The Spectre (aka the Wrath of God), to save innocent lives. One story involved him getting an ancient possessive spirit to leave a woman, which he did simply by glaring at the spirit and telling it "Get out of her. NOW." Said spirit promptly did.note For further proof of both sides of this trope, check out the Justice scene between the Big Red Cheese and the Big Blue Boy Scout in Big Damn Heroes.
Mary Marvel — who is just as strong as her brother, but nevertheless embodies "sugar, spice, and everything nice" — also qualifies.
Freddy is the only member of the Marvel Family who stays a child after he transforms, and certainly looks more adorable than Cap and Mary — but, ironically, he's the most brittle and cynical person in the family.
The Flash: Just because Barry Allen is an extremely optimistic and friendly person doesn't mean he can't kick your ass. He once threatened Aquaman when the latter insulted the original Wally West.
Bigby Wolf from Fables gets turned into a little girl during The Great Fables Crossover by Kevin Thorn. Gary the Pathetic Fallacy would not shut up about how cute Bigby was. This royally pissed off Bigby, who sulked for a couple of issues before sneaking up on a group of enemies that had his friends pinned down and slaughtering them literally bare-handed. This has the side-effect of breaking the spell on him and restoring him to his normal self.
Loki when he was reincarnated as Kid!Loki. Preteen God of Mischief willing to take on The Dreaded Serpent to save his older brother and the world too? Without the magical prowess and memories of his former self? Winning the hearts of Fangirls and the acclaim of Fanboys? Currently the star of one of Marvel's top books in under six issues? The kid does good work.
Tintin. A youthful, well-coiffed, baby-faced reporter who doesn't drink, talks to his pet dog, and upholds himself and the world to high moral standards. If you try to violate said standards in front of him, he will punch you through a wall.
From Death of the Family, while the "adorable" part is debatable, Damian takes it upon himself to just attack Joker directly. He gets captured, but he put up an interesting fight!
Hefty Smurf in The Smurfs, though arguably more badass than adorable.
Li Li Stormstout, the main character in the Warcraft Expanded Universe story Pearl of Pandaria definitely qualifies. On the adorable side, she's a young pandaren (which speaks for itself), heavily stylized on cute design, and much of a dreamer/adventurer character type. On the badass side, she is very proficient monk-style fighter and repeatedly handles her own mess, including stunts like returning thrown concoctions back to the sender with her staff. She also tends to end up on top in verbal arguments by means of intimidation or smart planning, and knocks an ogre captor unconscious by fooling him into drinking her entire jug of homebrew beer.
Green Lantern has Dex-Starr. He's a cute housecat, small, who really loved his owner. Her being murdered and two punks putting him in a sack and throwing him in a river enraged him enough to earn himself a place in the Red Lantern Corps, whose rings give them powers comparable to the Green Lanterns but geared to burn down everything... And he's the most sadistic and ferocious of all.
Miles Morales of Ultimate Spider-Man is a short, baby-faced, adorkable thirteen year old boy. He's also Spider-Man, with the associated power set.
Mia from Death Vigil looks and acts like an adorable teenage girl. She's also an ancient Eldritch Abomination so powerful that even the other abominations are scared shitless of her. Fortunately, she's one of the heroes.
The main cast of PS238 is composed of cute 10 years olds, with the appropriate mindset and innocence (for most of them anyway). They also have superpowers on par with Superman, Green Lantern or Plastic Man, to name but a few.
Pre-Crisis Supergirl is a cute-as-a-pie, sweet, innocent, smiling fifteen-year-old girl. She's also one of the most powerful beings in the galaxy.
Peter Parker from Spider-Man. Despite being incredibly agile and a super-powered daredevil, he's just so damn cute and fun when being in any situation with his life as a hero and a normal guy. The guy defines Moral Pureness for the entire Marvel community.