dark link from zelda 2, the joker from that batman nes game, the final three forms of the boss on ninja gaiden, man is he hard
https://www.youtube.com/watch?v=gGQ3SQSRoPI
https://www.youtube.com/watch?v=vswEyqq7PuQ
battle toads is really hard and never made it to the final boss
and talking about hard bosses, here is a list of really hard games from Angry Video Game Nerd
https://www.youtube.com/watch?v=rRW90lKwz4M