Pretty much any time Alice kicks into high gear qualifies. Her fight against the Licker is just the beginning.
Everything involving Nemesis. From the excellent costume and make-up effects, to the mini-gun and rocket launcher gunfights, turning against Umbrella, and even sparing LJ because he was a civilian, Nemesis gets plenty of awesome moments throughout the film.
Alice running down the side of a building. That stunt was done for real. Milla Jovovich's stunt double did the first half of the run 200 feet above the ground and Milla did the second half herself.
Near the end: "My name is Alice. And I remember everything."