I voted The Wind Waker. Unlike the Ganondorf battles in Ocarina of Time and Twilight Princess, his depiction in The Wind Waker conveyed pretty much everything I want from bosses and enemies in Zelda. In OoT and TP, Ganny was little more than an epic puzzle. In TWW, he was an epic, living, breathing enemy who forced you to think on your toes and adapt to his aggressive combat style to survive. It didn't quite have the atmosphere or longevity of the TP battles, but bosses are meant to be a test of your combat skills, which I felt TWW Ganondorf did a superb job at. It becomes impossible to damage him at some point, leaving you to team up with Zelda to strike him with a Light Arrow, then put a divine blade between his eyeballs. In the other two games, you can basically abuse one or two simple tricks to end him.
I've enjoyed all fights with Ganondorf so far, but gameplay-wise, The Wind Waker nailed it more closely for me than any other time. I may have some issues with the game itself, but the final boss was awesome.