I know it's been mentioned but Majora's Mask takes the prize for both... playing as Link alone it's stupidly hard to make it through the whole fight, and playing with the Super Deity Mask (or whatever) makes it stupidly easy.
The only boss I've ever truly come to hate was a dragon from a really old Amiga game called Dizzy and the Yolk Folk (or something similar)... there was a bit where you had to jump into a dragon's mouth - which, obviously, kills instantly - but at the LAST POSSIBLE SECOND, use a potion item to send it to sleep or something. I swear, the timing on this had to be pixel perfect... too early and you wasted the potion, too late and, well, you're dead.
Could have been because I was around ten at the time, but I actually cried because of that thing.