Mandatory bosses or optional? I'll pick from both but usually the optional superbosses are the hardest in the game.

Here are some I remember having trouble with.

Seymour Flux. (The third fight with him), FF X
I found this boss to be much harder than the Fourth Syemour fight. His party wide attacks hurt a lot.

Gogo, FF V
This is only if you actually decide to fight with Gogo. (you are supposed to do nothing. Hard hitting counters which lead to Gogo just going berserk on your party. Coupled with a time limit because you are underwater.

Zodiark, FF XII
Party wide spell that has a 1/3 chance of instant death (that is used liberally), along with the ability to become immune to your attacks is already quite the challenge. Add getting through the gauntlet that is the Henne mines in one piece and you have a tough boss.

4 Crystals, FF V
This boss is manageable if you know what to do, but if you don't then they will probably steamroll you with their powerful spells that they use when low on HP.