That's tough, but I'd have to go with...
Chrono Trigger
The Halo Series
Tie: Gears of War and Super Mario Galaxy
Chrono Trigger is just incredible: it has many, many songs that fit the mood beautifully. If you want some amazing music, look for Chrono Symphonic: a collection of fan-made remixes/orchestrations of Chrono Trigger. Incredible stuff.
The Halo series... say what you want about the hype, but the music in those games were fantastic. One of my favorite moments for musical design in video games is at the end of Halo 3. A track is playing as you progress through the last level, and when you get to a certain point, the last cutscene starts. The music flows directly into it, not breaking or pausing from gameplay to video. The music has been at a different spot for that last scene every time I've played it, and it still works beautifully each and every time.
I didn't expect much from the Gears soundtrack, but my cousin got it and told me to listen to it, and it is one of the best soundtracks I have ever heard. It's amazing, and fits the game perfectly, having a dark, apocalyptic sound while capturing the heroic feel of your mission. Fantastic soundtrack.
Super Mario Galaxy just astounded me. I never expected such epic and beautiful music from a Mario game: sure, the series has always had great music, but this sounded like an epic sci-fi adventure, while still encompassing the fun feel of Mario. From epic orchestra pieces to calming piano songs, this soundtrack is one of the surprisingly best soundtracks I have ever heard.
However, I have to give some honorable mentions here. The Final Fantasy series has amazing music: each and every game. Even X-2, for how much hate it gets, actually has a fantastic soundtrack. The Final Fantasy VII compilation, in particular, is awesome: the Crisis Core soundtrack is fantastic, and I don't think there's a Final Fantasy VII fan out there that doesn't shed a tear whenever Aeris' theme plays.
Beyond Good and Evil is another one that is more than worth mentioning, but all of us who were lucky/smart enough to experience that game know that the whole game is amazing in pretty much every way. All of you, play that game so you will be ready when the sequel finally comes out!
I would mention the Super Smash Bros. Brawl soundtrack, but that's just cheap. But it has orchestrations and arrangements of some of the best music gaming has ever known. 313 tracks of it. And they orchestrated the Tetris song. How can you go wrong with that? !?