My favorite boss is definitely Majora from Majora's Mask. That battle was pure epicness as was the moon sequence to get to the battle stage. Phenomenal experiance for sure! I mean, fighting a mask that grows arms and a face was bizarre and amazing at the same time.
My favorite mini-boss is Igos du Ikana (could you tell?) Aside from being a really cool character, my first time around I found it to be a tricky battle. Took me a little while to figure out I needed to shoot the curtains with the fire arrow cause I was getting creamed lol.