I know you list PC gaming, but if you have a PS2 around, then Castlevania: Lament of Innocence has, IMO, some of the best musical scores in any game I think I have ever played. Each of the 4-5 different major areas each had their own symphonic score that was very fitting with the overall theme of the area.
I also always have to crank the volume on my own home theater for the opening cinematic with Tidus playing Bliztball on Final Fantasy X. That game also had some pretty good music.
I do seem to recall way back when Doom 3 was about to come out, the developers talking about how they designed it with a surround system in mind, and were trying rather hard to create a creepy sort of atmosphere. With the recent release of the BFG edition, might be a good excuse to give it a shot if you haven't already.