Hmmmm... Notable favourites are:
LttP - General Boss Theme
WW - Molgera
TP - Stallord (2nd Half), Blizzeta (2nd Half), Ganondorf Duel
ST - Byrne
SS - Koloktos
Also, the Miniboss themes from Ocarina of Time and Wind Waker, and the Stalfos and Lizalfos themes from Skyward Sword, do they count?