I'm not really into the RPG genre, but I absolutely love this game. Quirky humor, simple battle system, good story and character development. I've probably played through it four or five times now, which is saying something as it's a rather lengthy game. Then again, I've owned a copy since it came out in the mid-90s, so I've had some time to play.
Also, for honorable mentions:
Star Wars: Knights of the Old Republic I and II
Donkey Kong Country 2
Legend of Zelda: Majora's Mask
Star Wars: Dark Forces
Super Mario World
Star Wars: Battlefront I and II