Specify the game, please? Because if you look at the section of the FF Wiki main page for all the various games, there are around fifty of them. If not 100 or more. Do that, and I'll help you if possible. OR check FF Wiki and search for "Superboss."
Pandaemonium Warden from Final Fantasy XI Online is regarded as the most difficult, as no player(s) of the game have ever legitimately defeated the superboss since its release.
After that, Yizamat of Final Fantasy XII has the most HP and takes even well-equipped players of the game at least an hour to defeat, possibly longer.
The Midgar Zolom from FF VII. He is just....cruel!
Damn you, Penance, damn you!!! (ffx)
ive beat midgar zolom at level 20 easy and got beta to boot, emerald and ruby weapons are the worst on ff7