Star Ocean 2, Vesper and Decus. The epitome of "That One Boss" battle. One of them has attacks with wide range and can petrify you, and the other spams fire spells that easily do well over your max HP without resistance. I mean, yeah, now I know how to take them out easily but not so much the first time through the game.

Persona 3, Sleeping Table. Only boss that really made me seriously level up/fuse better Personas. If you get lucky, it wastes it's turns on status or instant death spells (which are still dangerous), if unlucky it spams a hit-all fire attack and an Almighty spell that easily takes over half of your HP if not killing you outright. Of course, SMT games have their fair share of these kinds of bosses.