Oh, absolutely! ^^ While not particularly challenging, my favorite boss -- not just from TP, but from any video game -- would definitely have to be the four-phased battle against Zelda, Ganon, and Ganondorf. Excluding that, however, I really love the scale of the Stallord battle.
Also, I know that, in most circles, I'd get some flack for saying this, but I thoroughly dug Zant's shift into lunacy. With that being the case, the fight against him was -- for me, at least -- immensely entertaining. What are some of your favorites?