According to my theories, Ganon is not dead. Here's why:
Ganondorf died at the end of The Wind Waker when he was impaled in the head by the Blade of Evil's Bane, and turned to stone, thus ending him on the adult timeline. Unless... someone were to go down into flooded Hyrule and pull the Master Sword out of his head, and by some miraculous feat, he... stops being stone, and becomes Gerudo again, and then successfully gets back to the surface. Needless to say, that is never going to happen. As far as I know, Ganon is forever gone on the adult timeline. The Triforce was used to make a wish, and it is back in its resting place. Ganon does not have it.
On the child timeline, however, Ganondorf's body died when Link stabbed him through his Sage wound. Note that I said his body died. Remember how the Triforce of Power disappeared from his hand? I believe that he used it at that time to release his spirit from that now lifeless body, and now he is currently wandering around somewhere as a spirit, gaining power, and looking for a host. Now, since he is technically dead, a new Gerudo male will be born, I do believe. Perhaps when the time comes, he will possess this new male Gerudo, and Ganondorf will be back once again on the child timeline. Although I have another theory that next time we see him he will basically be a 3D version of ALttP Ganon, but I'm not going to go into that.
So what I'm saying is, Ganon is dead completely on one side of the Zelda... universe, and possibly able to come back on the other.