Ocarina of Time Ganondorf.
It's the first time we see him as human.
Nintendo decided to forego their standard "evil dragon-thing" bad guy and actually make Ganon into a character. The Dorf gets the most character development in Ocarina. We get to see how he lived as a Gerudo. We get to behold his conquest of Hyrule and his rise to power and the effect it has on the land and its inhabitants. We get to watch him scheme and plot. We get to witness his corrupting power lead to his fall to temptation and his resulting transformation into the beast Ganon. They made him human and then he lost his humanity and became the "Ganon" that is known to the series. It's an effective way to tell an origin story retroactively.
This is yet another reason why Wind Waker
sucks seems like it was shoehorned in to the Zelda series. For a game that is a direct sequel to Ocarina, Wind Waker Ganon completely disregards all this. He's not uncommonly referred to as "Ganon" in Wind Waker but he never appears as the pig lizard. More than that, Wind Waker's "Ganon" is too sane. Almost perfectly reasonable even and acts with kit gloves compared to other games. If this is supposed to be "Ganon" after inexplicably breaking out of the Dark World and wreaking so much havoc on Hyrule as a rampaging monster that the gods had no recourse but to get all biblical, he sure doesn't show it!
He should have appeared more as he did in Twilight Princess. Mad. Insanely Arrogant. Royally Pissed OFF. Exuding barely contained hatred and malice and unbridled rage that could explode at any moment! TP at least got that right. Unfortunately like so much of that game, Ganondorf is woefully underdeveloped. We don't get any insight into his motivations other than the obvious "conquer Hyrule again just out of spite." We don't get to see him plot and work his schemes. We have no sense of the relationship between him and Zant. We don't know what his time in the Twilight Realm was like or what the Triforce of Power has done to him.
His portrayal in TP is best in series. Although Ocarina does a good job portraying him as a cocky, self assured youth, TP is the only game to explicitly nail his portrayal and mannerisms and really solidly convey the intensity of Ganondorf's character. But Ocarina of Time is the only game for character establishment, building and development.
Wind Waker Ganon is too inconsistent for me to recognize him as Ganon(dorf).
... and in BotW he's a cloud
