My personal favorites would be
5. Legend of Zelda: Ocarina of Time (Incredibly memorable from the Goron theme,to the windmills,even the Korkiri {or however it's supposed to be spelled} Forest)
4. Super Mario Galaxy 2 (The orchestarted approach from Galaxy was great and made a whole lot better with a lot more vairety. Galaxys themes sounded mostly soft than loud and focused too much on the whole orchestra and not enough solos. Galaxy 2 added even more variety and the audio was better as well. A shame the gameplay isn't quite up to par)
3. Tomb Raider (Great themes very scary,intense,much like the game itself. Too bad it's mostly quiet and the themes only come on when you see a monster or unlock something)
2.Yoshi's Island (The great introduction,the catchy levels,frantic boss battles,and heartbraking credits,the OST transcends the gameplay by a longshot)
1.Super Mario 64 (When I reviewed this game I clearly said that I could've given the game an A+ on the OST alone.Maybe it's nostalgia but I just can't help but let out a small tear when I hear that Final Battle with Bowser. The staff roll is incredible and I still sometimes find myself whistling the Bomb-Omb Battlefield theme. Strangely enough it's only game from my top 10 still on the list)
Honorable mentions to Super Smash Bros. Brawl,Super Mario Galaxy, Mario Kart 64, Tomb Raider II,and BioShock