I think OoT Ganondorf is by far the best rendition.
(Spoiler warning!)
Personally, I think the development of OoT Ganondorf is the best. This is for the simple reason that he plays such a role in the story and changes the world dramatically, which was quite the plot twist after getting the Master Sword. The events afterward give Link a lot of character development and motivation to save Hyrule, where his evil showed more impact on the characters than it does in any other game.
Ganondorf, already a king, is clearly not satisfied with the level of power he has; so he sets out to pry all the remaining pieces of the Triforce from their live containers to gain the pathway to the gods, and become a god/demigod.
OoT Ganondorf's acts of thievery, mass murder, pillaging, regicide, attempted genocide, and physically warping the landscape are a direct attempt to leave the world in shambles and upset Link and Zelda, so he can lure them to obtain their pieces of the Triforce. OoT Ganondorf really takes this to a personal level, and he ruins Link's childhood, surrounding Link's home with monsters to torment and kill the Kokiri, and murders Zelda's parents and destroys their home. As young Link, Link explores the diverse and beautiful land of Hyrule and meets its inhabitants, before they too, are ripped away from him. Ganondorf's entire plan rests on the notion of tormenting the people of Hyrule until they need a hero to save them. What's truly evil is that becoming the ruler of Hyrule is not even his goal, and that the power of being a tyrant is only a step in his plan to enable him to make people suffer enough for them to lead the hero to him.
We don't see much of character development in TP Ganondorf, nor do we see him be very evil at all. He's hardly there for most of the game, which doesn't allow him to have much of an impact on the story. TP Ganondorf doesn't use psychological warfare against his enemies like he does in OoT, and he's not nearly as Machiavellian. He doesn't really show any sort of evil schemes or grandiose demonstrations of evil as he does in OoT, either. Sure, TP Ganondorf looks more "badass," but isn't that mostly because of the graphics?
To me, it's definitely the actions that make the villain, and OoT Ganondorf outshines all other Ganondorfs in this regard astronomically.