Ocarina of Time was my favorite, but with Wind Waker and Majora's Mask following closely. OoT made so many great, memorable melodies that perfectly fit each place/function of the song. Majora's Mask had a ton of fresh new songs, with great emphasis on the music. And Wind Waker had some really nice songs too, all very smooth, flowing, and original.
To me, Twilight Princess didn't do too well with music. I was disappointed by the wolf songs immensely, because that was the only music-related part of the game. Four of the songs were used before, and the other two were ones I'd never remember because you only play each song once. Almost all of the other songs were just remixes of the old ones, anyway. And buying the soundtrack is hardly satisfying; you only get six of the many songs from the game. It's not that all the music was terrible and hard to listen to, it just didn't live up to my expectations or the standards set by previous games. It sounded alright.
Link's Awakening also did pretty well with music. Although I never really got through it enough to judge the music, what I did hear was pretty good and catchy.
So here's my final list:
1) OoT
2) WW and MM
3) LA
4) TP