I have to say, I'm staying with the Ocarina of Time and Majora's Mask OSTs which I happen to own. For Nintendo 64 games, both of them had beautiful music <3
I like the music from Wind Waker, too. And from Link's Awakening and I guess any other LoZ GBC game (ah, nostalgia XD).
Also, the music from the Dept. Heaven series never fails to be beautiful. And the Touhou music can't be forgotten, either, especially when you consider that only one guy composes all of it.