Ocarina of Time's was a ridiculously watered-down version of the earlier Phantom Ganon battle, so I can't even label it as good. The Wind Waker's was kind bland gameplay-wise, but had great presentation. Twilight Princess's, while easy, was a well-crafted battle and had great presentation, as well.
I'm going to have to go with Twilight Princess's Ganondorf fight.
If we're strictly speaking Ganondorf, then I choose The Wind Waker. Seeing the King of Evil dual wield blades was a welcome change in pace as was his altered demeanor. As the flood gates burst in the background, Ganondorf's plans figuratively sunk as Daphnes Nohansen Hyrule touched the combined Triforce first. I actually felt remorse for Ganondorf because until the very end, he seemed to be reformed, seeking retribution for what he perceived as wrongs against the people of Hyrule rather than advancing his own selfish ends.
If the Ganon portion of battles is considered, however, then my vote goes towards Ocarina of Time's. The Ganondorf portion of the battle was disappointing especially after a significantly better Dead Man's Volley with Phantom Ganon in the Forest Temple. The Ganon battle largely ameliorated these wrongs. Not only were the flaming castle remains an appropriate environment for the climax but losing the Master Sword spiced up the first portion of the duel. Slaying Ganon was a rewarding experience opening a culminating cutscene that is among the best I've seen in any videogame.
My favorite battle with Ganondorf, the Gerudo not the Pig, would be that of Twilight Princess. For me, despite the ease, I didn't feel the battle itself was anti-climactic at all. In fact, it carried a very "epic" vibe with it which resonated throughout the four-step battle. That isn't to say playing tennis with Ganondorf in Ocarina of Time or fighting a duel to the death with the fat very muscular maniac in The Wind Waker were boring or non-epic themselves, just that TP's fight carried the epic vibe through and through.
Just the scene before the very first battle with him gave chills down me spine:
The Ganondorf fight of OoT is easy as heck and a little disappointing but still memorable. The GANON part of OoT though is one of the most epic fights in the series and I will NEVER forget the first time I fought Ganon. If we're talking strictly Ganondorf though, Twilight Princess wins out for sure. Fighting on Epona was AWESOME.
Definitely Twilight Princess. It gave us battles on every corner of combat and was very epic.
Next would be Ocarina of Time. Another epic battle, and the volley was kinda interesting without Z-Targetting.
Last would be Wind Waker. Maybe it was because of the clunky combat and the poor graphic depiction of where his sword was when he blocked...but it felt like fighting Zant with a sword (which is to say, a kid who has no idea what he's doing). Not to mention it was waaaayy too short and easy. BBBBABBBBABBBBABBBBA *cutscene* BBBBABBBBABBBBA *cutscene* RA
Twilight Princess Ganondorf battle was the epic one I've battled. It was intense, cruel, dark, hard, and epic to achieve to defeat the Dark Lord. The music and scenery was perfectly fit into place with battle between Link and Ganondorf. Total epic with this battle.
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.
The entire Twilight Princess fight, no contest. The only thing TP failed at was being difficult, but other than that, it gave fans (and by fans, I mean me) everything they wanted in a Ganondorf fight. Puppet Zelda brought back the classic tennis we knew from OoT. Ganon was the inevitable form that we knew we'd have to fight, allowing us to go beast on beast with the thing. The field chase put Zelda and Epona at our side, making the adventure truly feel like a knight and princess were protecting their kingdom, and that last fight... that last one on one epic sword fight with the G-man himself. It was all I ever wanted
Everything about these fights were epic. The emotional feel of the cinematics (Midna! Don't be a hero!), the atmosphere of the music (an evil version of Zelda's lullaby!?!) the impact of the lines being said by the characters ("Shadow has been moved by light it seems, how amusing"), right down to that stormy sky. Everything set the stage of making you feel like that epic hero you were supposed to be.
Now, don't get me wrong, the other fights were fun too and did really well in their areas, but I think TP does the best turning Link into the hero we like to view him as and turning the story into that kind we like to see. Epic.