Whats your favorite story in a game ever?

[Grey Acumen]

That's tough to say. Chrono Trigger was amazingly well woven, but there was a lot of stuff just left hanging.

Twilight Princess will always be big for me. It was good enough that didn't notice how linear the game was until I was just about to beat it.

Baldur's Gate is more for for the compilation of sub stories that you come across that the overall plot of the game. I also don't play without fanmods.

Majora's Mask was really good for the storyline, in many ways, far moreso than Ocarina of Time.

I can't really think of any other's that come close in terms of how good teh storyline itself was.