Already mentioned in the literature section, but (because it bears repeating) Reepicheep from the The Chronicles of Narnia films. Modeled after Errol Flynn and voiced by Simon Pegg, Reepicheep goes mouse-to-man several times... and wins! Even though he is as cute as Lucy says (he prefers "courageous, courteous, or chivalrous"), he's a force to be reckoned with. He even tried to take on an army of Telmarines by himself! He easily manages to be the best part of both of his movies.
In battle, Quorra of TRON: Legacy knows how to kick ass with her kickboxing and dogfighting abilities. When she's not fighting however, she's naive and has a childlike-innocent view of the world.
Yoda, probably the most iconic example of an old Badass Adorable ever. Short height, big cute eyes and his wisdom knows no limits. And yet, one of the most powerful Force users and sword fighters of the Star Wars universe.
Anakin Skywalker in The Phantom Menace. Born of the Immaculate Conception, incredibly sensitive to the Force, a mechanical genius on his spare time and one of the best podracer pilots in the galaxy, not to mention his instant mastery when it comes to pilot a Naboo royal starfighter, destroying the Trade Federation's mothership thus putting an end to the conflict on Naboo in the process. And he was only 9 years old.
The Ewoks. Cute fluffy teddy bears in hoods. Fierce warriors (with teeth) willing to take on the Stormtroopers with nothing more than slings and rocks. They kick some serious rear.
Rocket Raccoon. The cutest little raccoon you'll ever see... and then you realize how good he is with guns.
Groot as well. He's basically a living tree and a kind creature... but don't piss him off. This is turned up to 11 with Baby Groot in the sequel, who is six inches tall, utterly adorable, and can beat up full-size humanoids.
Wonder Woman is a kind, beautiful, warm-hearted and compassionate ray of sunshine who single-handedly sets out to fight World War One because she refuses to watch innocents suffer and die under the cruelty of tyrants, literally plowing through those who would victimize the weak like a hot knife (or sword) through butter.
From Master and Commander, Midshipman Blakeney. He's this utterly adorable curly-haired twelve-year-old, who... gets his right arm amputatedbut doesn't let it slow him down, becomes something of a "fighting naturalist," and leads a group of men more than twice his age into battle, thus helping secure a decisive victory over the HMS Surprise's archenemy, the Acheron. His inspiration is Lord Nelson, also missing an arm.
Bumblebee in the Transformers Film Series. Bright yellow, mentally younger than most of the other Autobots despite being physically around the same age, and over the course of the trilogy; racks up a Decepticon body count second only to Optimus Prime himself. In Transformers: Dark of the Moon, he even gets more weapons and armor to symbolize his evolution from guardian to full-fledged warrior. Yet, he still has his blue eyes and still talks through his radio; never once losing his connection with the younger audience of the movies.
Sir Trenton from Racing Stripes is a horse that has no problem beating Stripes senseless before the big day, with the help of his army.
Mako Mori in Pacific Rim, a cute Japanese survivor who wants nothing more than to have the heads of each and every Kaiju on a pike.
Laura from Logan, an adorable 11 year old murder machine who knows how to rock a pair of pink cupcake sunglasses.
Kate (Mary Elizabeth Winstead) from the prequel to The Thing (2011). Intelligence and bravery aside, she has been described by a review as "looking like a cute teenager trying to buy booze with a fake ID rather than an actual adult."
Tae-goo from The Good, the Bad, the Weird is such a wacky, klutzy, utterly adorable buffoon that you just wanna pinch those chubby cheeks of his... but don't, or he'll shoot you in the gut. He is, after all, the most fearsome criminal in all of Korea.
Keanu from Keanu is an adorable, little kitten with big, black eyes...that's also able to karate chop guys 100x his size.
Alita: Battle Angel: Alita is a small, wide-eyed, sweet, adorkable girl who loves chocolate. She is also a re-embodied cyborg special forces soldier with elite cyborg martial arts who smashes and dismembers cyborgs many times her size.
Detective Pikachu from Pokémon Detective Pikachu was this before his accident, being strong enough to defeat Charizard and scar its face. Not so much after his accident, where he lost both his memories and his power. He gets his powers back in the climax of the movie, hitting a Howard Clifford-controlled Mewtwo with a Volt Tackle strong enough to send him into a building.