Whether we particularly enjoy his presence or not, Ganondorf has shown himself as a series staple of sorts. The bearer of the Triforce of Power and he who invaded the Sacred Realm makes him an extremely powerful asset in the series canon. As it has been said several times above, the King of Evil seems to have met his end in both potential timelines (the split timeline theory was pretty much confirmed by Mr. Aonuma). It does not escape me that he may one day be found crouched in the depths of the Great Sea. Of course, whether or not he is able to be reveived is a matter of debate, though, in a Zelda game, I think it is quite possible. I, personally, would love to see the Gerudo King of Thieves revived and brought back to the world above the waves long after Hyrule has been rebuilt in another far away land. Would he assume control of Wind Waker's world, using it as a foothold to eventually invade "New Hyrule"? Would he be met with resistance by the locals? Would another Hero rise from WW's territory? Would the "New Hyrule" Link be forced to seek him out? This all would make for a rather intriguing storyline.
We must remember that TP's Ganondorf may not necessarily be dead, so we may expect to see him in a later game. Remember, Ganon is present in the 2D games, making for potential placement after the events of Spirit Tracks and Twilight Princess. (Yes, they could have transpired before SS, but that would mean the events took place before the forging of the Master Sword and founding of Hyrule. Possible? Yes. Likely? Far from it.) This means, he could either be reincarnated or revived. Of course, the Zelda timeline is a rather touchy topic, and it is best to be debated elsewhere.
Might we see Ganon(dorf) in Skyward Sword? The possibility cannot entirely be ruled out, though I do not suspect we will see him as a major villain. Perhaps we will see his earlier years, as SS has been said to lead up to the events of OoT.
Will we see Ganon in a game again? It is more than likely that we will.