I dunno... the votes for the hardest bosses in RPGs would have to go to...
A) The end bosses in Valkyrie Profile (the ones in the Seraphic Gate)
and
The Dark Aeons and Penance from Final Fantasy X International
...
But overall, I'd say the final area in Might & Magic VII (the one with all the little droids running around firing particle beam weapons at you, just as you enter the starship) was ungodly insane. The new version of Chaos for the FF1 Wonderswan is no joke either; they gave him two new attacks. A Kefka-ish Fallen One style attack, and a Death To All attack.
