Variations of the finale appear based on your overall item collection percentage (time taken to beat the game doesn't count). See below for the added ending scenes and their requirement.
SPOILER WARNING!
Don't read on if you want to see the endings yourself.
Complete the game with less than 75% items collected:
Samus watches from atop her gunship as the Artifact Temple burns, contemplating her future before leaving the planet.
Complete the game with between 75% - 99% items collected:
As Samus watches the Artifact Temple burn she'll remove her helmet. We then see a close-up of her face before she departs the planet.
Complete the game with 100% items collected:
Keep watching after the credits roll for a hint of Metroid Prime's fate.