No-one's mentioning the Gerudo Valley theme enough. So, here goes:
5. Wind Waker title theme. Probably less enjoyable than the theme on the main sea, but I spent too much time on the sea (!@#$% you, sailing) so this one wins.
4. Great Bay theme. Oh yeah. Nicely mysterious.
3. Grotto theme, same reason.
2. Lost Woods theme. Seriously, takes a simple six note riff and actually makes it pleasant to listen to for hours on end. WIN.
1. GERUDO VALLEY THEME. !@#$% YEAH.
Seriously, so many reasons to love this song. It's flamenco, it's guitar-based, there's a nice trumpet section, it perfectly represents the area, it's so dramatic and instantly recognisable, and it's LOVELY.
Dragon Roost Island gets a very very honourable mention, because it's !@#$% awesome and I'm a fickle !@#$% and decided to throw in three different OoT songs instead of considering quite how awesome WW's soundtrack was simply because of how much sailing pissed me off.