Ganon is the beast form that Ganondorf, the Gerudo man ('human'), transforms into.
Depending on the game, generally that is the case, but in older titles, those before OoT, it was only Ganon the beast, and he did not have a human shape.
Nowadays, Ganon is generally seen to be the true form of the man Ganondorf, who was twisted by the dark realm, or transforms with his dark magic.
In some titles however, the name is used interchangeably. In the Wind Waker, all of the people in the game refer to him as 'Ganon', not Ganondorf despite him being in human form the entire game. He himself, however, introduces himself to Link as Ganondorf, not Ganon.
Currently in the series, Ganon and Ganondorf are the same entity and are interchangeable, but generally Ganon is only used when referring to his beastly boar form.
More reading can be found here:
http://www.zeldawiki.org/Ganondorf
Any other questions that are not clear I will be happy to try and answer.