My favorite Zelda song is the Fairy Fountain theme/ File Select theme and all of its variations throughout the series.
[video=youtube;6h5w6pwD8Ic]http://www.youtube.com/watch?v=6h5w6pwD8Ic[/video]
This is what I think of when I think of Zelda. This music to me is so nostalgic and iconic to the series, and I die of happiness everytime I hear a new variation
Close second: WW title screen/ Credits theme. What a brilliantly put together theme
Oath to Order, followed closely by the Dark World theme from A Link to the Past. All the songs on the list, and in the rest of the series for that matter, are pretty fantastic though.
Ballad of the Wind Fish(LA), Gerudo Valley, Saria's Song, Serenade of Water(TP Remake) Shop theme(OoT), Song of Healing, Song of Storms, Song of Time(Temple of Time theme). Hmm, Hard choice. Seeing as this is not a multiple choice poll, I'll go with:
The Song of Healing:
[video=youtube;WXnWfx6bIVE]http://www.youtube.com/watch?v=WXnWfx6bIVE[/video]
Nah jus' kidding, for me from that list the New Wave Bossa Nova is the best, for a song needed to progress its just so funkaay. Also it, coupled with the Great Bay as a whole make the Temple not look bad at all.
Otherwise it has to be either Mt Crenel from The Minish Cap (=EPIC) or Hyrule Field at Night from Twilight Princess.
My favorite zelda song of all time would actually be Spirit Temple. It has that Muslim\Egyptian\desert theme to it. And I really like the Muslim\Egyptian\desert style of music.