My favorite boss is that golem thing from phantom hourglass(forget name) the fight was forgettable, sadly, but I knew how much fun it was hammering up to pound buttons.
My least favorite is the first Zelda boss(apparently boss names don't matter to me) he is just hard, because I never bothered with the magical shield. Or, the arrow until after the fight.
That's all!
I should have said this earlier, but plot wise, the bosses are different. My favorite is vaatti,(never beat th Minish cap) because of his dark personality. My least favorite is ganon. I know, he's the main enemy. But now, it's like he's the ONLY enemy. I hate that they stopped adding new antaganists.