I would have to say Wind Waker. Firstly because it was so different from same old fantasy setting music seen so often in previous games, and other similar titles such as Final Fantasy. It did a great job of capturing a different feel and culture for the game, and for each island.
And I genuinely like the very celtic sounding title screen song. Very different from almost all the other sequels.
My favorite Zelda soundtrack happens to be Spirit Tracks'. Spirit Tracks had an excellent score. It's the only one I've downloaded and have on my iPod. The music in Spirit Tracks had unique tracks that really helped get a feeling of the events that occurred. The greatest ones from the game, in my opinion, would have to be the ones from the Malladus fight, both phases, and the Sacred Duet.
1 Ocarina of Time its has wonderful music all through the game I love the Water and Shadow Temple's and Ganon's Castle the most.
2 Majora's Mask love the Oceanside Spiderhouse'Woodfall Temple and Majora's Mask battle.
3 Wind Waker Foresaken Fortress'Earth Temple and Phantom Ganondorf music:yes: really stands out in this game!
4 Spirit Tracks I loved all the Temples music and the Tower of Spirits.
5 Phantom Hourglass the Final fight with Bellum and Bellumbeck I adore this music its some of the best boss battle music I have ever heard!
I like the Wind Waker's soundtrack the most, because it had many memorable tunes and I think the music gave out a lot of emotion. Second place for me would have to be Twilight Princess.
As I just got reminded, I must agree on the WW soundtrack as well. It was a very creative and nice soundtracks. But for me, If comparing the games of Toon Link and their music, my fav one is ST.
WW, only because of the staff credits music. It was so beautiful...it really made you feel as if something great was truly lost, but at the same time it gave you hope that something better would eventually come along.