As someone said, the Mother Brain from Super Metroid was great. I played that game for the first time about a year and a half ago and felt a great sense of accomplishment when I finally finished. That said the final boss was much easier than some of the previous bosses in that game.
Shodan, and comedy version gladso, are two of the greatest computer game antagonists. But I rate them so highly for the conversations and insults throughout the games rather than the final fights themselves. Their personality and negative relationship with you is what make finishing them off so much more satisfying. It's good killing agent Navarre for similar reasons... and the fact you can choose from so many moments to kill her.
I have a fondness of Phantom Ganon from OOT because it seemed like such an imaginative boss in such a ground breaking 3d game. Riding out of paintings and requiring the player to try and spot the authentic Phantom Ganon painting. I'm not sure if it still stand up as well but I'm fond of it.
Vega... He calls you ugly and climbs up the background before jumping down to scratch your face. And in most iterations of street fighter you can choose can play as this mf.
Bowser in Super Mario 3d land. There have been many great Bowser battles and it's hard to pick a favourite but 3D Land felt the most satisfying and entertaining. Not just a straight up fight but a chase through an fun level packed with platforming fun.
















