I would have to say the whole battle with Ganon/dorf in TP. It was a lot more epic than the OoT battle in my opinion, being able to go toe-to-toe with Ganondorf in sword combat instead of just battle light balls back at him. We got that part out of the way with the Zelda battle. The whole idea of being forced into a ring to fight him while Epona and Zelda watch on was just great. The music was very epic, and the close-up of Link and Ganondorf locking swords was a really memorable moment.
The beast Ganon part was great too, with the eerie tribal-like music and the disappearing act. It was also a nice touch to add in one of the earliest things you learned in the game, wrangling goats, as a way to beat the final boss. Who knew you'd use that technique to stop Ganon?
I did enjoy OoT's fight with the beast Ganon, but really it was a bit dull. Yes he was big, yes he was creepy, yes he was imposing, but really he just stood in one position and pivoted around a bit. He really didn't do much other than look impressive, but TP's Ganon was all of those qualities and he also posed a serious threat in his disappearing and charging.
The horseback battle was great as well. It seemed a natural thing to have to do way back in OoT that I felt was missing. You had Link on a horse, you had Ganondorf on a horse and yet there was no classic jousting or horse-dueling battle. People are always saying how TP didn't feel like the medieval Zelda that most enjoy, and yet I would say that horse / sword battles are a prerequisite of medieval knights and the like.
I'm surprised more people didn't like the TP battle after all of the complaining from the Spaceworld GameCube footage of the non-WW Link / Ganondorf fight. People wanted that for years and were diappointed when they didn't get it in TWW. We finally got it in TP and it was spectacularly done, and yet people don't seem to like it. To each their own I suppose...
So, with 2 Ganondorf fights, a Ganon fight, and a Zelda posessed by Ganon fight, I'd have to say it's the winner.