Dobby. He's saved Harry's sorry ass quite a few times, disarmed/attacked several wizards, and says the most awesome line an elf could ever say: "Dobby has no master!!!" He even died like a Badass! Hit by a knife thrown by a crazy chick you just dropped a Chandelier on while apparating three other people out of the domain of Voldemort. Though to some, he's not EXACTLY adorable.
Reepicheep: A cute two-and-a-half foot talking mouse with honor, dignity, and the ability to successfully take on an armed opponent twice his size. One of the few characters from Narnia aside from Aslan who shows up in three books; at one point, he even sails over the edge of the world.
Lucy: The entire Telmarine army skidded to a stop in mid-retreat, scared stiff of one small adorable girl smiling sweetly at them from across the bridge (their only escape route) while brandishing a dagger. And that's beforeAslan stepped up beside her.
And in the film version of Dawntreader we finally get to see her in action, rather than just as an informed ability, and we find out why.
The Archive is a prepubescent girl who shows her Badassitude when she's attacked by Red Court vampires while she's moderating a duel. She grabs a piece of anti-life being used and, with sheer force of will, thrusts it into the vamps heads and torsos, vaporizing them. In a later book she's attacked by a dozen fallen angels in an area cut off from magic. Using the little magic she could store in her tiny body she starts taking them down, two at a time, even while Harry carries her away. She even makes a point of trash talking the angels, although she's not that good at it. She's only captured because the demons take advantage of her low body weight and gas the whole area. She's also very fond of cats and renders official documents in crayon.
Mouse is pretty awesomely adorable, too. Sure, he's a dog that's around four foot tall at the shoulder, but he plays the goofy Gentle Giant act up so well you forget about that and just want to snuggle with his big fuzzy self. Then he starts glowing and makes an eldritch horror run away in terror after ripping the back of its foot off. He also garners more respect from a powerful Sidhe noble than his "master" does.
The series' originalBadass Adorable, Karrin Murphy. Blond, five foot nothing, with a cute little button nose, and she's proven so incredibly badass so very many times that she'd need her own subpage to list all the examples.
Temeraire, although unusually for the trope, the badass is the most immediately obvious (he is a dragon, after all), and the adorable comes out in his interactions with the other characters, particularly with Laurence.
Redwall's cute fluffy animal Kid Hero characters. D'awww, fwuffy ickle mousey. Who just happens to be wielding a BFS. Big for a mousey, anyway. From the average human perspective, it'd be about the size of a kitchen knife at best.
Otto von Chriek from The Truth is this crossed with The Woobie — he's a reformed vampire who prances around in his neat suit and his thick Uberwäld accent, taking photographs and accidentally turning himself into dust every five minutes. But when his friend William gets in trouble, Otto casually beats up a team of muscled goons and scares the living bejeebers out of their boss, all while sporting a longsword in his chest and still maintaining his adorable Funny Foreigner front.
The Lord of the Rings: Hobbits. For creatures the size of human children, they prove to be surprisingly adept at arse-kicking.
Pippi Longstocking is a cute, quirky eleven-year-old... with incredible super-strength. Given that she lives in an otherwise mostly mundane world, we never really get to see just where the limits to her strength is, but she is perfectly capable of overpowering stampeding bulls, angry tigers and fierce sharks without the slightest difficulty. As in lifting the shark in the air while she's swimming, without difficulty. And she scolds it.
Charlie McGee, the eponymous Firestarter; a cute, little, blonde-haired girl who even gets called "button" more than once, theoretically capable of cracking the Earth in two when she comes into her full power. Certainly already capable of vaporizing a man with very little effort.
In The Pale King, Leonard Stecyk is an excruciatingly upbeat, kind, and hard-working bully magnet. He's also the only one who rushes in to save his wood shop teacher from dying of shock and blood loss after an accident with a machine. His little apron keeps his clothes from getting drenched in blood, and he makes a perfectly-tied tourniquet on the fly.
Twelve-year-old, pony-tailed Kate Wetherall carries around a bright red bucket full of weapons, crawls through air vents, and can kick a Ten Man's ass any day of the week.
To some extent, Constance Contraire also fits this trope. Yes, she's not quite adorable, and certainly doesn't have the cheeriest disposition, but she can kick some serious butt hair-pulling and leg-biting.
The treecats in David Weber's Honor Harrington series are cute, cuddly, and great with children. They also can read minds and will turn into steel-clawed, near-unstoppable furry buzzsaws of death and destruction when they detect someone planning to harm those they care about. A treecat has only two categories of enemies: those that have been appropriately dealt with, and those that are still alive.
Gazzy and Angel from MaximumRide.Sure, they're cute and all, being the youngest members of the group, but Gazzy can blow you up with the MANY explosives he keeps somewhere in his clothes while Angel can effectively control your mind
In the Rainbow Magic series, Rachel and Kirsty are very young and cute, but they defeat Jack Frost every time he causes trouble.
Diana Tregarde. Barely five feet tall, and compared at one point to a music-box ballerina. She can take you apart with karate, a gun, or magical combat.
Spectral Shadows is full of animal characters, both feral and anthro. As such, this trope is inevitable.