Main character - Link because he is such a hollow shell that you can see yourself in his shoes. Excuse me Princess.
Story- Final Fantasy II SNES (Better know as FF IV) Leading a man through his loss of faith in his career, his King, himself, and friendship to be born again as a confident Hero fighting for all that he loves. My favorite game in the FF series and most likely my favorite story in gaming.
Gameplay - The best game you've had the pleasure to control. Even if the rest of the game sucked.
Musical score - Final Fantasy III SNES(Better know as FF VI) Each location and major character had it's/his/her own theme. They really drew you into the game. Despite lack of voice acting, the themes played through the music would set the tone for each situation, conversation, etc. Who doesn't remember Kefka's theme.
Setting and atmosphere - Silent Hill 1 & Bioshock are tied here. They both use a great mix a visuals and sounds. One using the PS1's lack of power to it's benefit and the other using current HD systems to it's benefit. Putting you in cramped spaces with trouble around each corner.
Intro - Uncharted 2. The train scene was awesome. It puts you straight into peril and makes you fight to safety for the game to begin. (Bioshock was also great. Playing the demo of that intro made me go out and buy the game.)
Ending - I've got a three way tie here. Zelda Wind Waker, Shadow of the Colossus and Super Metroid. WW for it's awesome final battle, Shadow for it's final heart wrenching end, and Metroid for the final battle/escape.
Online modes - Rainbow 6, working with 5 other guys to silently take down terrorists and save hostages.
