Final Fantasy VII. I remember there was a boss toward the end that was hard af to defeat. Also, I believe that there were other bosses that gave you special materia and/or weapons. One of the best games EVAR!!!

 

Tales of Xillia 2 EX Dungeon is nuts, you need to be well prepared or you won't last more than 2 minutes. on top of that you need to complete certain tasks in order to advance.
here is a good explanation of how it works.

 

Final Fantasy VIII, Ultima Weapon. A fun boss, but you can make him a pushover if you use Squall's limit break a few times



What makes him so annoying though, is his light beam attack, so have Revive with you.

 

Can't say "hard optional bosses" without mentioning Kingdom Hearts. I spent a good deal trying to beat Sephiroth as a kid or beating all of the data battles in Kingdom Hearts II.

I found Jevil not that hard actually. You'll die a couple of times trying to figure out his patterns but you'll be done with him in a jiffy.

As for turn based RPG superbosses, I hate them. Most of them have more to do with grinding than skill.