I dont know if anyone has mentioned these ones yet, but they are EXTREMELY HARD!!!
First, the SOMBRERO GUY that you fight at the end of the third level in a really obscure NES game made by Milton Bradley called Time Lord. I DARE you to try beating him without a turbo controller.
Secondly, and even more difficult is the final boss of Ninja Gaiden II. He has like 4 INCREDIBLY DIFFICULT forms that you have to fight in a row. You'll have a hard enough time trying to kill just one of these f***ers, but THEN, after you've lost all your damn health on the previous form, your health carries over to the next. TRY beating him without using emulator savestates or exploits - I dare you!