Hardest final boss if you're clueless: Terranigma. That is, if you have no idea how to block. Probably wouldn't be possible to kill him anyway, but it's sometimes funny to watch people scream in panic over it. ;
Hardest bosses I've run across so far.. The Four Abyss Gate Guardians in Romancing SaGa 3, but the second time around. (Before you fight the last boss.) Aunas and anything associated with him are permanently set in my mind as 'PURE EVIL.' It took me a while to get to the Fairy Village, and it took me DAYS to get to the Fire Palace. (I followed the Black Butterflies, as best as I could, for a day or so. Then, I just resorted to walking in and out randomly of exits. Heh.) Anyway, as far as the second Aunas battle..I cannot begin to tell you people how many savestate loads I did. I cannot imagine trying to beat him fairly on a SFC.
The others were pretty much as much of a pain as he was, but not QUITE as much. Though, I must say that Byuunei was particularly harsh. -.-;