I'd say the final encounter against Bower in Mario 64 would be one of my picks for best ever. Loved the organ music, and it was so satisfying spinning the joystick around so that you could gather up enough force to throw Bowser at the bombs: Super Mario 64 final Bowser fight - YouTube <-- I wasn't as brave as the player in this vid though. I always waited for Bowser to run to me, then flip over him, and grab his tail that way. Got him closer to the bombs too, so that's a plus.
There's a few from Yoshi's Island that I liked too, but I think the one with the crow, the one with the guy who's pants fall down after you hit him, and the Bowser battles are my faves. I also liked how you could skip the piranha plant boss fight if you hit it with an egg before Kamek has a chance to use his magic on it. If you do, Kamek's reaction is hilarious.
I liked the fight against Phantom Ganon in Ocarina of Time. Thought it was so cool when he pulled his face off and when he would run in and out of paintings. Also, volleying the energy blasts back and forth was fun, and really satisfying when it finally hit: The Legend Of Zelda OOT - Phantom Ganon Boss Battle - YouTube
Uh, that's all from me for now.
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