One word: resurrection.
It's quite possible that Ganon(dorf) would be brought back by another individual, with or without the Triforce of Power - I sincerely doubt that the ToP would be entirely necessary for him to live again.
Next, while Ganondorf is arguably dead in WW (he turns to stone afterall, so we can't tell, but we can most probably assume since he has a sword sticking out of his forehead), I don't think there is any doubt that this is the case in TP. He is seen dying, and I can almost certainly assume that he stays that way should he be left alone. The thing is, however, it's entirely possible for him to come back. They attempt to kill Link in order to perform a resurrection for Ganon in AoL, afterall.
Yeah thats basically my theory. What I was referring to was that Ganondorf as a human is likely to not return or be a part of many future games because of how the games are set up. Here's how I figure this...
We'll take a look at the Child Timeline. Starting with OoT, Link is sent back and presumably tells the king of Hyrule about Ganondorf's evil plans. Sometime later, he is sent to trial. We see this trial in TP, so one would assume that TP comes after OoT with nothing in between them to alter this process on the timeline.
Then, we look at the game that most people put directly after TP on the Child Timeline: A Link to the Past. The backstory of ALttP talks about Ganondorf, as a human, gaining access to the Sacred Realm and touching the Triforce. Upon doing this, he wished to rule the Sacred Realm. That is when the SR, along with all its inhabitants, and Ganondorf as well, were all transformed. The SR became the Dark World, which became overrun by evil creatures, and Ganondorf became his beast form Ganon permanently.
Now if you take all of this into consideration, you realize that the BS of ALttP speaks not of the events of OoT, but events which have to take place sometime later. Not only are the events of OoT completely separate from those talked about in ALttP, but Ganondorf didn't even gain access to the Sacred Realm on the Child Timeline. In that game, Ganondorf was able to access the Triforce and escape the Sacred Realm without being sealed. In fact, Ganondorf was sealed in the Evil Realm at the end of that game, but on the Adult Timeline, which would not have ever happend on the Child Timeline and thus never have happend in the history of events before ALttP. The BS of ALttP tells of him making his wish, being sealed, and then being transformed. Therefore this must be a different event. That would mean that the BS of ALttP is the only story that has not been made into a game, and the only place that it would fit would be between TP and ALttP.
This is where my theory comes in that Ganondorf probably did not die at the end of TP. Somehow, he may come back, but if he does I feel that the only tale to be told of the man known as Ganondorf would be the one explained in the BS of ALttP. All games after that included beast form Ganon. Now if they add a game onto the Adult Timeline, then you have to look at the fact that Ganondorf did not have the Triforce of Power upon dying. At this point, he did have magic, but not the power to keep himself alive from a sword stabbed through his skull. Therefore, if they were to revive Ganondorf in the Adult Timeline, I would think that he would be revived into another form. That form would be his beast/pig form, even though there are no more games after WW on the Adult Timeline (for the exception of PH and apparently ST).