That is a tough question. off the top of my head I would say song of storms, but I also like Midna's Desperate Hour, the Skyward Sword Main theme. There are many others that I also like. I really can't pick one favorite song from Legend of Zelda.
1. The main theme/credits theme for the Wind Waker. It's so well put together, and simple, and so catchy, and it just never gets old. It gives me so much nostalgia
2. Great Fairy Fountain/ File Select. I dont understand why not many people appreciate this song for what it is. I believe its the song in th 2nd most number of Zelda games (I think). It's fantastic. When I think of Zelda songs this is the first one that comes to mind. And I love how Nintendo can always bring it back and vary it in creative fantastic ways