I must admit all of the bosses in OOT are fun to play...
Gohma is a cool, yet very easy boos to fight. I'm kinda tired of fighting her over and over again, because the battle isn't even exciting when you beat her over 5 times...
King Dodongo is another easy boss, but it's a very creative one. I think it was a little hard to figure out how to stun him, but then, it became a piece of cake...
Barinade is an exciting boss fight, you have to run all the time while throwing a boomerang to it's body to stun it. Cool, cool fight

.
Phantom Ganon is a very fun boss fight, yet hard when you fight him for the first time (I must admit I lost around 5 times when the first day I fought him).
Volvagia is a very repetitive fight, a very easy boss, kinda fun, and it also reminds you to the Whack-A-Mole game.
Morpha is a hard boss fight when you first fight him/her (I don't know its sex, if he has one...). I'm glad I beated it on my second try... a great battle, I think I'll never get tired of it.
Bongo Bongo it's a fun battle, especially because you play on a drum. Kinda hard when you only have the 30 arrows quiver (I finished with one arrow! 0_0).
Tiwnrova is a very easy battle,but repetitive, and you kinda get bored when waiting to both sorcerers sisters to throw magic.
Ganon is a piece of cake, not that fun, and it's strange that you can kill a final boss with almost every weapon.
However, GANONDORF is a medium-ish battle (I must admit it's phantom is harder...), and an exciting and fun one. So my vote would go to ganondorf as my favorite boss of OOT.