Majoras mask. One of the most immersive games I've ever played and that I cared about the characters (and cried at the ending when the marriage happens) speaks volumes about the game. For main storyline I would put OOT.
Though I do prefer perfect dark, I would still rate goldeneye above it just because it changed how people did the FPS genre. There are games today that don't even come close to what rare did back in the late 90s.
Then there are the million of other great games, conker, shadowman,resi 2, blast corps, lylat wars. Too many good games to choose from!
Edit: Just remembered- body harvest and episode 1 racer. Without body harvest there could be no GTA as we know it today, not to mention that the game was cool. What other game has you hopping to russia and mowing down zombies with a combine harvester?