"When Ganondorf transforms [in OoT], his human face is pulled away and only the pig remains, it can't be hidden anymore." - Satoru TakizawaOn another topic, I had always assumed that Ganondorf/Ganon had some level of separation between them. My first game was OoT (though by the time I finished the game I had some knowledge of previous titles), and when Ganondorf transforms into Ganon at the end (and a new title card is used to announce it) I assumed Ganon was different on some level. His more simple animalistic form (compared to the human Ganondorf) to me suggested something more pure, some unlocking/tapping of triforce power.
However recent games with Ganondorf have either omitted Ganon (wind waker) or portrayed him differently (Twilight Princess). So in conclusion I would say that the definite relationship between Ganondorf and Ganon hasn't been fully explored, if there really is one.
take that as you will.
Also, in WW, Daphnes refers to Ganondorf as Ganon until he sees that he's in his Gerudo form.