I like the A Link to the Past: Dark World theme and the Great Sea music in Wind Waker a lot. In general, I like most of the music for Legend of Zelda games though.
To be honest I haven't played nor officially owned any of the Zelda games.
Until October this year[Twilight Princess]. I'd say I like all the music. [even though it's been awhile since I last played the game.]
If I was to try to make a choice, I would end up posting a ton of links and videos like what everyone else has done in this thread. A LOT of the music in the games is amazing.
I just love the music that plays when you stun a boss in Twilight Princess. Its so epic I can't help singing along: "Dun dun dun dun dun dun duuuuun! Dun dun dun dun dun dun duuuuuuun! Dun dun dun dun dun dun dun dun du-di-dun!" I love it when it plays in Spirit Tracks too (when you get the invincibility power up in multiplayer).