Well, from all the games I have, there are 2 or 3 games I never finished because I couldnt beat the final boss.
So my vote goes to that witch from Banjo Kazooie.
The first part is okay, then you have to evade her fireballs, within a split second, you must jump up the wall thingy, and press two buttons to shoot eggs at her 0_0, and hope that you're not late before she shoots you once and you fall, thats right, forward off the wall having to start all over.
I once got to the flying part, exidentily hit Z and stomped myself to death ;_;
So close.