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.
It may not have been 100% confirmed in game or by the developers, but it's very, very,
very heavily implied. Let's look at the games that feature Ganon(dorf):
TLoZ: Ganon's debut, he steals the Triforce of Power. Link kills him and reclaims the Triforce. TAoL makes it clear that Ganon is completely killed, not just merely defeated.
ALttP: A thief named Ganondorf steals the whole Triforce and becomes the Demon King Ganon. Link defeats him and obtains the whole Triforce. Ganon is likely not killed, because AST shows potential of Ganon being revived, as does ALttP's official timeline placement before TLoZ.
OoT: Ganondorf, king of the Gerudos, attempts to steal the Triforce, but the Triforce splits upon him touching it and he is only granted the Triforce of Power. He is defeated by Link, and the seven Sages seal him away. Though he is sealed, he still possesses the Triforce of Power.
OoS/OoA: Ganon is revived by Twinrova, but because the revival went wrong, Ganon is a mindless beast. He is short lived, because he is killed by Link yet again. Ganon did not possess the Triforce at all.
TWW: Ganondorf has escaped his seal from OoT, and still possesses the Triforce of Power. He reunites the three pieces of the Triforce and attempts to use its power to grant his wish, but King Hyrule beats him to it and he is defeated by Link. He is left far below the Great Sea turned to stone and Triforceless with the Master Sword stuck in his head, washed away with old Hyrule.
FSA: A Gerudo man named Ganondorf breaks his people's taboo and steals the trident and Dark Mirror from the Pyramid. By stealing the trident, he becomes the Demon King Ganon. He is defeated by Link and sealed in the Four Sword. He never had any part of the Triforce, nor was the Triforce even seen or mentioned.
TP: After Ganondorf tries to steal the Triforce in OoT but fails, he is captured and sentenced to death. However, before his execution, he is granted the Triforce of Power, most likely through divine intervention. This is because he was
supposed to obtain the Triforce of Power, but that event never happened, so the gods or even time itself corrected what was destined to happen. With his newfound power, Ganondorf kills the Sage of Water, and the remaining Sages act quickly and seal him in the Twilight Realm. Many years later, with the help of Zant, he escapes the Twilight Realm and takes over Hyrule, but he is killed by Link. While some people debate it, it's quite clear that he's killed here, as the Triforce of Power leaves him, and the whole scene really drives home the idea that he is dead.
With all that in mind, how could there possibly be only one Ganondorf? There has to be
at least two. In my timeline, there are three:
1. FSA
2. OoT/TWW, OoT/TP
3. ALttP/TLoZ/OoS/OoA
Anyway, I think Nintendo has made it clear enough that there is more than one Ganondorf. And while they may not have came out and said it directly, they also haven't directly said that there is more than one Tingle, Malon, Dampé, etc., but we all assume that there is anyway, don't we? Why don't we assume the same for Ganondorf?