Ok a bit more time so here are some of the best I can think of just off the top of my head
HL2 - Path of Borealis, you don't hear much of this track in the game, but the full thing is epic
SMOD's Welcome to C17 remix, I used to sit in the menu of the original SMOD (awesome way more fun way to play through the HL2 campaign IMO) because I wanted to hear the entire song before playing
Ocarina of Time is the only Nintendo game I bought the soundtrack for, here's a couple favorites:
But other Zelda games have a few outstanding tracks, like this one from Twilight Princess:
More FF7, 2 of the best boss battle themes OF ALL TIME
A personal favorite of mine, up there in my top tier of 'Entire soundtracks that are all so good I can't pick a favorite soundtrack' along with Bastion and FF7,
Superbrothers: Sword and Sworcery EP which was an amazing game no one freaking plays.
More to come later as I start to remember the best of the best.