Final Fantasy 9 springs to mind
It's not only the individual pieces that are good, but it amazes me how cohesive the entire thing is, they way melodies and ideas intertwine and are revisited and indicitive of the plot, to the point that you can interpret certain plot points from the sound track alone! For example, there are two jesters introduced early on, who turn out to be two major antagonists through a lot of the game. Their theme tune is upbeat and jestery, I guess, but underneath it, as an inconspicuous part of the music, an ominous theme that usually precedes boss fights is being played on the organ! Little things like that, when you've played a game for ~years~ and you only then realize them just amaze me and really make me appreciate how much attention to detail has gone into this. ~This~ is why Nobuo Uematsu is a genius. :p