I don’t know about soundtracks as a whole, but some games have great individual songs. I think my favorite was from Ultima: Quest of the Avatar. There’s a bard you talk to in the inn in Brittania, who says something like “We have waited for you for a very long time”, and then the background music changes, presumably to the song he’s playing for you. Sometimes when I’m playing, I linger in Brittania just to hear the song.
Another great one was in the original Final Fantasy. Most of the start of the game is pretty easy, up until you get to the Marsh Cave, which will usually kick your butt unless you spend a lot of time grinding before you get to it. You basically need to save your game at the entrance, go in quick, run from almost all monsters you encounter, hope you get lucky rolls in the boss fight, and then run back out, and fall back to the save every time it doesn’t work just right. And the music for the cave levels is this frantically quick piece that just sets the mood perfectly (the same music is later re-used for the Mirage Tower, but it isn’t nearly as scary there, since by then you’re pretty powerful).
As it’s own thing, I would go with the Bastion soundtrack. Some parts of it are a bit slow and repetitive for my tastes, but on the whole it’s great and the opening in particular is fantastic.
Taken together with the game, though, I would say Chrono Cross. The game itself has plenty of problems and indulges in some of the worst JRPG excesses, but it does an incredible job with creating a sense of place and the soundtrack is (ahem) instrumental. The El Nido archipelago feel like a living, breathing place and it’s largely because the soundtrack does such an excellent job of creating that breezy, island living feel. It makes me feel like I should be lying on the beach listening to the waves and sipping a Mai Tai.
I actually ended up downloading the Transistor soundtrack and I don’t skip them when they come up in winamp, great stuff.
It was a long time ago, but I recall the music for the snow board level of MDK as being very epic and impressing me thoroughly.
The opening theme from Total Annihilation still sends shivers down my spine, the actual soundtrack is a great fit for the game, but doesn’t really stand on its own.
The pseudo monastic chants from Chaos Gate are incredible. Haven’t touched the game since 1998, but still occasionally listen to them. I even put some of them on my road trip CD.
Absolutely the sound track to Fahrenheit, or Indigo Child, as it was known in the US. Admittedly I played that game for far too long (hey! I was young!) but yeah, totally atmospheric.