Jenova's theme, definitely, and One Winged Angel. Goes without saying.
Gilgamesh and X-Death/Exdeath/Ux--Daeeph(whatever you prefer to call him) had fairly neat-o themes too (FFV). Similarly cool was the 'Sorceress battle' theme from FFVIII and FFVII's regular 'boss theme' (Still More Fighting).

But One Winged Angel really does take the cake for quality and emotive impact.
*Hands One Winged Angel the cake*

Even if its lyrics are recycled from Carmina Burana. Why shouldn't today's best draw inspiration from yesterday's best?