From a cut-scene, it would have to be Tales of Symphonia for the ending. That cue is just so epic. It makes me want to go out and buy an old Gamecube and a copy of this game just so that I can hear that again.
As for in-game, Bioshock's music was amazing, Halo's was very good, Call of Duty 4 in Chernoble was also good, Mass Effect comes to mind, Little Big Planet, Metroid Prime 2 for the title screen, SSX 3 had a great licensed soundtrack, the new Prince of Persia was good once the lands were healed, and that's about all I can think of off the top of my head.
Zelda would be on this list if Nintendo would just use some of its wads of cash to actually pay for a real orchestra to play their music! The Zelda theme is one the best in gaming, and it's squandered due to it being put together on MIDI files! Twilight Princess would have been 10x better if they had just gone out and gotten a real orchestra.