Adventures of Link is the greatest, although as a kid I never got much further that the part where you get the hammer. The red wolves that chuck axes at you are the worst. Boo for Wind Waker being at the top. The sailing in the game was amazingly boring and I eventually got too annoyed with it and quit when you had to sail around and get all the triforce pieces. Second would either be LTTP or OoT.
Edit: Glad to see Wind Waker's reign was so short...