Hardest boss? I would say Red from Mega Man X7, but he's more annoying than hard.
Probably that guy at the end of the game Sunset Riders for SNES. (it was something Rose, can't remember his first name) You had to shoot him, well, his barrier first, then him, but of course, there was at least a hundred different enemies helping him out from every possible window/door. And even when you beat him, he pulls out a bulletproof chest plate, then fights you again on the spot. (Even with all the power-ups, it was impossible to keep them with all the enemies firing at you)