I have quite a few tunes stuck in my head (not on an iPod or anything - just in my head):
Beast Malladus Final Boss (ST)
Ganon Final Boss (OoT)
Last Six Hours (MM)
Ganondorf Final Boss (TP)
Outset Island (WW)
Tower of the Gods (WW)
Credits (TP)
Great Bay Temple (MM)
Stone Tower Temple (MM)...