Jo McCormick from Big Bad Beetleborgs fits this perfectly (especially since she's a pre-adolescent girl).
River Tam of Firefly. Basically she's a genius girl of about seventeen who is insanely talented in every single thing imaginable, and starts out very innocent-looking until she suddenly beats up multiple enemies at once with her crazy martial-arts-style moves. On top of that, due to experimentation done on her by the government, she is mentally unstable, usually being very calm and soft-spoken until something sets her off (and we don't always know what that something will be). This is most obvious in The Movie, Serenity, when she first beats up a whole bar full of enemies, and later when she locks herself in a room with a bunch of crazed zombie-like people, just one of whom could kill several ordinary people, and kills them all.
While not a superheroine/villainess, Sam Puckett is widely acknowledged as the toughest kid of either gender in her school, took down a bully twice her size and ripped the chain lock off a door when in pursuit of Freddie in "iKiss". Did I mention that she was towing a kid heavier than herself at a full run at the time and wasn't out of breath? Of course in both cases cited she was in Unstoppable Rage mode at the time but still. As for the cute part, she's a teen and when she cleans up is quite easy on the eyes. However, asking her out may result in having your thumb broken...just ask Gibby
Shelby. Described by one male character as smoking hot, yet still somehow adorably cute, and by a female character by something along the lines of, "I'm sure your butt is super cute." And she's a world class mixed martial arts fighter.
Macy Misa on Jonas is very cute and petite and acts very girly but she also plays for every sport the school has (basketball, football, hockey, baseball, bowling) and has enough brute strength to be considered The Big Guy in their Five-Man Band.
Male Example: Wyatt Halliwell from Charmed. Seriously, as a kid he's able to fight demons already. And the one time we see him fight as a young man he looks like one of the Backstreet Boys but is the destined wielder of Excalibur and wipes out an entire room full of upper level demons just by raising his hands.
Supernatural has an episode revolving around an actual, working wishing well. One of the wishers was a small boy who was being bullied. He got super-strength, along with a bad temper.
Kamen Rider Den-O gives us Hana, who when her natural age looked quite cute and unassuming, got even cuter after she got reduced to a child. However, she's got Super Strength and isn't afraid to use it. To show the extent of it, she punched Momotaros threw the side of the Denliner without even trying.
Smallville's Tess Mercer is a Dark Action Girl who does not believe in Waif-Fu. Most other girls on the show dance around their opponents and use a lot of kicks. Tess prefers to just punch you in the face.
Super Sentai usually has one of these among it's yearly cast. Typically female.
Sherlock: John is definitely adorable and short, being 5'7, though he's older than Sherlock. But mess with his friend and you're screwed. He kicked two villain asses and threatened death on one of them. And look adorable while doing it.Not a survivable move if a detective's being messed with. Mess with him, and be prepared to get killed by a mild-mannered doctor.
Caroline from The Vampire Diaries. A lot stronger and tougher than she looks once she becomes a vampire, and cute as hell.
Moze in Ned's Declassified School Survival Guide, though, like Sam Puckett (mentioned above), she's not a superheroine. She's cute-looking and easy on the eyes, but she's beaten up Ned and Cookie multiple times, shoved Ned against a locker during her "anger" phase of the Five Stages of Grief when she lost her backpack, flipped Loomer and was able to send him and his posse running just by threatening to beat them up, and was able to beat up the entire boy's wrestling team without breaking a sweat.