While Exdeath's gimmick of wanting to end reality by bringing the existence as a whole into the void was never really the most compelling goal (in Final Fantasy V, a game that wasn't really all that compelling to begin with), Neo Exdeath makes the list solely on the virtue of looking like a high-ranking Berserk apostle. Just look at this dude. This is monster design by way of the electric kool-aid acid test. There's a skeleton, he's got some kind of the Predator in there, a bunch of ladies, and a big ol' bat up top to bring it all back home. Neo Exdeath looks like something Ultraman would fight if Ultraman was created by Jan Švankmajer.
Throw in the fact that the Neo Exdeath boss fight actually has separate attack patterns that revolve around his jigsawed appearance, and it's a neat battle.