Main character - Link. Archetypal hero, not super character driven, just a classic hero on a quest to save the world.
Story - Earthbound. It hit every emotional note a game can hit. It was sad, funny, poignant, and uplifting, often all at the same time.
Gameplay - Super Mario Sunshine. Just absurdly fun, simple but innovative all at once.
Musical score - Probably Final Fantasy 6.
Setting and atmosphere - Flower. I know this isn't what you meant, but the environments were perfect and made it possible to basically turn your brain off while playing and have a totally visceral gaming experience.
Intro - Blue Dragon. From the way the splash screen pops up as you run down the hill, to the awesome, "LAND SHARK! I WILL NEVER GIVE UP!" sequence, the first 10 or so minutes of this game are 100% unmatched ever.
Ending - Fable 2, to me, had the most awesome ending in history. Never mind the DLC that kind of messed things up, the entire childhood dream sequence and the moral choice that followed it were very, very good to me.
Online modes - This is a hard one. Timesplitters 2 was probably my favorite online gameplay experience in terms of pure fun, so I guess I will go with that?
