I think one of the hardest bosses was mizar on Jet Force Gemini, the second time you fought him. You don't even know if you're doing the right thing until about twenty minutes of doing it gets you through the first part of the battle. Thank god the rest was pretty easy.
Another one was Grandia Xtreme's final boss, and it's not cause of his abilities, well, not entirely. The game was so amazingly unbalanced that by that time, I had gotten used to relying on one character for all my hits (play it and you'll know who), and the game is ridiculously easy, right up until him. Not to mention there are four or five floors of monsters you can't skip, who conviniently soften you up for him. Not to mention he has about seven other things to hit at the time, which are all hitting you. Not to mention he has the most irritable (half because it doesn't fit him at all) voice. Not to mention Kroitz. Goddamn Kroitz! He's not in the final battle, but jesus christ, I hate him anyway.