Another vote for Twinrova. It's a shame the twins chose to pursue two diametrically opposed magic elements or they might have had better luck against the fellow with the reflective shield...
For me it was hard to choose. But for me I just LOVE fighting Barinade to point that I look forward to fighting him when I come up to that part.Not to be gross but I like how he bleeds green blood and how he dies. Bongo Bongo is my next pick.
I personally loved fighting with every boss in the game!!! But if i had to choose one it would be Ganon! It was so awesome when that cutscene comes where Link stabs Ganon in forehead!!!
Actually I enjoyed Morpha. I know it sounds weird, but somehow I got enjoyment out of hookshoting her, then slicing her to bits, especially when you put the final blow to her.
I liked Bongo Bongo. The Shadow Temple overall was very accelarating. And to fight Bongo Bongo you constantly needed the Lens of Truth on. Unless, of course, you are one of those people that has incredible timing and turns it on just before he slaps you of the drum.
I had the most fun fighting Volvagia. It was like a Whack-a-Mole game with the excitement that LoZ delivers. Not the mention epicness that the music added to the fight.