Don't state this as an absolute quite yet. This hasn't really been confirmed (at least, not yet).
The only instance where I'd say Ganondorf's death is truly debatable is at the end of TP. If you place FSA sometime after TP but before ALttP, and don't subscribe to the multiple Ganondorf theory, the only explanation of Ganondorf's presence in FSA and/or ALttP that I can think of is that he must have not died at the end of of TP.
Spoiler Warning! Please do not read the next few paragraphs or watch the linked video if you have not finished TP.
http://www.youtube.com/watch?v=EmxxIZapJXc
In the above video, Ganondorf was stabbed in the stomach with the Master Sword, but that still has not killed him. He mentions, "Do not think this will end here," which seems to imply that either he will return, or that he will be avenged. He is still breathing well after being stabbed, which leads me to believe he is still alive. Even after Zant breaks his neck, he is still standing. He never falls to the ground, and if you look closely -- as the camera zooms out -- you can almost see his chest moving a little, which leads me to believe he is still alive in some regard.
To be fair, though, at the end of OoT, Ganon was stabbed in the head repeatedly before being sealed away, yet he was still alive. However, he lives on well after the Great Flood. I believe he no longer possessed the Triforce of Power after being sealed, hence why he cannot turn into Ganon in TWW. I think this absence of the Triforce of Power is because the Hero of Time took the ToC back with him as a child, which "broke" the Triforce in the AT, hence why Link has to gather the pieces in TWW. The Triforce fragments are distributed now on the CT, as is illustrated in Ganondorf's attempted execution.
Now, I do note that the Triforce of Power disappears from his hand. I admit that that is very strong evidence against this argument. However, he appears to lose the ToP every time he is defeated, whether or not he is sealed or killed. At the end of TP, it is possible that the Triforce restored itself and was returned to the Sacred Realm, because that is where it is located before and during ALttP. This may mean that the disappearance of the Triforce is merely associated with Ganondorf's defeat, and not necessarily his death.