Balto: Jenna is willing to fight a furious bear far larger than she is and has no qualms with standing up to Steel, something many of the male dogs in the film are too afraid to do. Sadly, she ends up fading into the background in the other two films. Her daughter Aleu in the second movie also gets to be badass, but unfortunately she quickly falls into Faux Action Girl territory.
Big Hero 6: GoGo Tomago and Honey Lemon are just as integral to the eponymous team as the other male members, and prove to be skilled combatants with their abilities (super speed and chemical explosions, respectively) in battle.
Bolt has Penny (the onscreen version, anyway), particularly in the opening. Mittens has her moments as well.
Maria Posada. When Manolo and Joaquin start a swordfight over her, she picks up a sword and disarms them both in a single move. And that's before the bandits show up. During her travels, she has learned fencing and kung-fu.
The Adelita Twins. Both of them due to having fought in the revolution as soldaderas.
Brave: Merida, who is awesome with a bow and arrow.
The Hunchback of Notre Dame: Esmeralda, who, during the Festival of Fools, successfully fights off several of Frollo's guards, and is the one to rescue a wounded Phoebus from drowning the river after he's shot by said guards in a later scene.
The Lion King: Nala is a very strong fighter, and a fierce hunter. Even as a cub she's shown to have considerable skill, always trumping Simba during their bouts of playful roughousing. ("Pinned ya!")
The Little Mermaid: Ariel was actually the first Disney Princess to be proactive. She outwits a shark, rescues her Prince, and destroys two of Ursula's minions. While Eric does save her in the end, there's no denying that this girl was the one who set the stage for more strong female leads in Disney.
Shrek: Princess Fiona has a BadassAction Girl moment in the first movie, but kind of stays behind in the second and third movies. Then the fourth movie rolls around, and the trope makes a glorious comeback.
Space Jam: Lola Bunny, a basketball player so talented that even Michael Jordan notes that "the girl's got some skills".