Regardless, in general, the name Ganondorf refers to his human form. He may have been referred to as Ganon once or twice, but aside from that, he is known as Ganondorf. His beastial form is always referred to as Ganon.
In LttP they mentioned that Ganon was once a human named Ganondorf so it would seem that Ganon would be referred to his beast form while Ganondorf human form; I guess to avoid confusion at times.
He is referred to as Ganondorf through the entirety of OoT, until he transforms and the battle title card gives him the name Ganon.
In WW, his humanoid form is once again referred to as Ganondorf throughout the game. (When the King speaks of Ganon, he is talking about the monstrous transformation that clawed its way back into Hyrule, forcing the Goddesses to flood the land.) The same goes for TP, through until he transforms into Ganon as the second stage of the final battle.
As for chronology, OoT has been confirmed as the first story (disregarding The Minish Cap, which does not have Ganon/dorf, or indeed even the entire Triforce), and WW and TP are parallel sequels to OoT. All other games (except MM, which comes chronologically before TP) would seem to follow WW or TP in their respective timelines.
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Wrong, in OoT, he is refferred to as Ganon, and is in WW as well, hell, I think he even refferred to HIMSELF as Ganon. Oh, and Four Swords Adventures was confirmed to be the first Zelda, and does have Ganon in it.
Four Swords Adventure retold the story in the desert of Ganondorf's transformation into Ganon and is a sequel to Four Swords which is a sequel to Minish Cap so how can it be the first?
Interview with Eiji Aonuma, Miyamoto's top dog, guy that works with him on the story, and is top producer of Zelda series.
BB: That’s something that, you (Bill Trinen – Localization Team) and I have talked about with the release of the Zelda compilation disc, cleaning up some of the spellings like Ganon, and making sure everything is cohesive. Maybe that’s an American thing – us wanting to know how it all works together. I guess that leads me to my next questions. How do the Links in The Four Swords Adventure relate to the overall story line? Or is it just a subchapter or something like that?
EA: The GBA Four Swords Zelda is what we’re thinking as the oldest tale in the Zelda timeline. With this one on the GameCube being a sequel to that, and taking place sometime after that.
Note that that interview is now three years old. It has since been retconned by Miyamoto to taking place much later, with Minish Cap taking the title of chronologically first.
Really, the creators themselves don't seem entirely clear on their own (theoretical) timeline, but it is generally accepted that Miyamoto confirmed OoT as the first chronological appearance of Ganon/dorf.
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