I think Ganon is a demon... one who was worshipped by Ganondorf's surrogate mothers, who after giving birth, named their son after him. He is a spirit of greed, who manifests himself physically as a boar-like monster. I think he was lurking within Ganondorf since birth, he is the source of Ganondorf's magic and the driving force behind his motives.
In the early chronology(
OoT,
TP), he is a wild, rage-filled, porcine beast; like incredible hulk he doesn't have very much control of himself, but sometime along the way, Ganondorf permanently mutates into this form, with his original mind and personality intact, as seen in
ALttP.
Of course, this is just my opinion, I don't really have much of a source.