I can't possibly pick an overall best from the whole series, so I'll sort by the games I've played.
Ocarina of Time: Saria's Song. Childlike, gets stuck in your head, can be danced to. Pure bliss.
Majora's Mask: Final Hour. The song that plays when the clock is one hour to doomsday. Very depressing. Shows that there is no hope left. This song plays no matter where you are in the world when the final hour comes. It's very poignant.
Wind Waker: The Great Sea. Heroic, awe-inspiring. It really makes the world feel grand and large when you sail across the enormous ocean. I love this song.
Twilight Princess: Hidden Skill Training. Sounds exactly what one would think of when training for battle. Sounds a lot like a marching song.
Skyward Sword: Title Theme. This is pretty much the only song we even know of, but it's already a favorite. Extra points because it's what you get when you play Zelda's Lullaby in reverse, only played by an orchestra! Skyward Sword will also be the first time the soundtrack will be completely orchestrated, so I look forward to the rest of the soundtrack.