I think ALL oot bosses were really cool but i think the number one is...
ganon from OOT.
yup, it wasn't that original, thought-provoking or even that hard, but ganon looked so awesome and thrashing his swords (excuse me, his sai's) was so breathtaking. Also ganondorf (human form) was very very cool also.
Oh man, i doubt twilight princess will one-up oot, but i want it to so bad.
P.S- I noticed that the environment during the final fight is so awesome, the sky looks SO COOL.