I also would have to say The Bone Dragon from Paper Mario: TTYD. You can only encounter him When you complete the Pit of 100 Trials, that means u have to clear 99 stages with enemies (unless u r lucky and there are a few stages without enemies) without beeing able to save in between or go to a hotel to sleep to recover ur wounds.
And in the 100th stage the bone dragon comes and he is then even harder than the final boss of the game.
You are only able to do that when u have loads of potions, and leveled up like crazy. And when u die u have to do all 99 stages again!
U dont have to beat him to finish the game but i was lucky enough to beat him =)