1. Slash - The Boss in TMNT IV Turtles in Time on the Prehistoric Stage
2. The Indian Dude who would say "ready for pow-wow" in Sunset Riders.
3. As Fonix said, the end final bosses in Ninja Gaiden Trilogy. You get to the final boss(es), 3 phases, and no health regen. Best part is, if you die in any of the phases, BACK TO THE BEGINNING OF THE STAGE. And yes, I'm talking about without saving your state on a rom, and also the fact that the ninja gaiden stages are 10 times harder then the bosses lol.
and finally
4. As Lobelia Mk. IV said, Sephiroth. Would really love to know how he became so popular considering he just whines and babbles, offered no challenge in the game whatsoever, and apparently comes in any name possible in any mmo. SephirothX, XsephirothX, DarkSephiroth, CloudXSephiroth, SephirothEX, just drop it already -_-