I found that Total Annihilation had the best stock music ever. Totally mood specific. Also Homeworld (1 and 2) had excellent music. ANd if anyone here ever played Grim Fandango they'll know that the film noire be bop jazz was excellent in it.
I don't often play other music with games. I find if Im not paying total attention to the music it gets old without me actually enjoying it.
But I think the ultimate game/music combo is Listening to "Ride of The Valkyries" while playing the Omaha beach map on DOD.