Zeromus would definitely be my favourite for the music and how awesome and gross he looks, plus the part before where everyone's prayers revive Cecil and the gang, showing just how many people Cecil has befriended and positively affected during his quest.

There's quite a few bosses that were memorable for how unique the battles and strategies to beat the bosses were, especially for the time it was released: Baigan, the Magus Sisters, Rubicant, Asura, Odin (one of the few battles where Rosa shouldn't be healing), Behemoths (if only I noticed that casting magic provoked him into using Maelstrom), Bahamut, the combined elemental lords, the CPU, and Plague Horror.