Zeldas Lullaby is my favorite. Very soothing. I also like Dragon Roost Islands theme and the main Wind Waker theme.

Thanks for mentioning this Nate. These were the final results.

25.) The Hidden Village (Twilight Princess)
24.) Farewell Hyrule King (The Wind Waker)
23.) Temple of Time (Ocarina of Time)
22.) Overworld (Legend of Zelda)
21.) Termina Field (Majora’s Mask)
20.) Title (The Wind Waker)
19.) Title (Legend of Zelda)
18.) Cloud Tops (The Minish Cap)
17.) Dark World Death Mountain (A Link to the Past)
16.) Molgera (The Wind Waker)
15.) Title (Ocarina of Time)
14.) Spirit Temple (Ocarina of Time)
13.) Overworld (Spirit Tracks)
12.) Legendary Hero (The Wind Waker)
11.) Midna’s Desperate Hour (Twilight Princess)
10.) Tal Tal Heights (Link’s Awakening)
9.) Song of Healing (Majora’s Mask)
8.) The Great Palace (Adventure of Link)
7.) Ballad of the Wind Fish (Link’s Awakening)
6.) Dragon Roost Island (The Wind Waker)
5.) Gerudy Valley (Ocarina of Time)
4.) The Final Hours (Majora’s Mask)
3.) Ending / Credits (A Link to the Past)
2.) Stone Tower Temple (Majora’s Mask)
1.) Dark World (A Link to the Past)

It is an excellent list. I enjoyed watching the live stream.
The only one I reaaallly didn't like is the Ballad of the Wind Fish. I found it grating. Too bad Ocean theme of Wind Waker didn't make it instead.