Picking three is dumb, but whatever. I'll probably go past three, but that doesn't really matter.
Metal Gear Solid 3 On the one hand, you have some of the most powerful and emotional scores to come out of a film composer (HGW). On the other hand, you have the energetic and occasionally nerve-racking (in a good way) jam-fests from Mr. Hibino. All the music is wonderfully varied but at the same time very fitting.
Katamari Damacy No two tracks are alike, but at the same time it is all very fun and happy and wonderful and more positive adjectives. The composition is fun and energetic, and somehow the vocals work brilliantly (unlike just about every other game made). Yu Miyake, the sound director, said they crafted the songs to match each vocalist's specific talent, and you can tell it paid off.
Simcity 4 + Rush Hour This may seem like a strange choice; nobody really lists this game on any list. However, the soundtrack is probably one of the best to come out back in 2003. About half the music is fast-paced and busy, while the other half is more laid back. Some of it is jazzy, some is more hip-hop-like, while even more goes into electronica and orchestral. However, all of it portrays the city life fantastically, fitting the game more accurately than most other soundtracks can only dream of.
Beyond Good & Evil The game nobody plays that everyone loves, and one of the major drawing points is its soundtrack. Containing some of the most touching themes in recent memory right alongside some of the strangest and more imaginative songs in a game. Another one that gets the vocals right. It is a real shame so few people picked up the game, since I'm sure this soundtrack would get more mainstream attention had it been more popular.
There are others (Super Metroid, Ace Combat 5, Ikaruga, Napple Tale) but I'm lazy and don't really feel like explaining all of them.
