I think mine would be
1. Sheik's Theme.
It has that sad feeling to it, as though all was lost, but then it seems like, little by little, hope is gained.
2. Zora's Domain
I like this one because it has that tropical feel to it. What I mean is that it seems as though the Zoran race doesn't have a clue as to whats going on out of the domain.
I totally think that Nocturn of Shadow should not have been in the game! If you play all the other songs, it seems so dark in comparison!