Well, although WW might seem ambiguous because he turns to stone, Aonuma confirmed that he did die, and that the reason that he turned to stone was so that the game could keep its G rating, as well as flowing with the games vibrant and childlike nature (the graphics etc etc).
Twilight Princess on the other hand is open to speculation: I like to think that he died after Zant did the whole neck snap thing. The Triforce of Power fading is also a possible indication for his dying.
Speaking of the Triforce of Power... it is possible (I'm not sure if this theory has been discussed much here) that the piece grants Ganondorf some form of immortality of extended life. In OoT, Ganondorf is totally thrashed about by Link, and then stabbed in the forehead after transforming into Ganon. However, he remains alive, and the Sages need to seal him away in the Sacred Realm. In Twilight Princess, when the Sages go to execute Ganon, he does not die, as the Triforce of Power activates. He then proceeds to go on his little rampage before being banished to the Twilight Realm. At the end of Twilight Princess, after Link deals the finishing blow (sticking the Master Sword right through Ganondorf's gut), Ganondorf remains somewhat confident that his war between Light and Shadow will continue. While he is obviously weakened, he isn't in a state of dying until the Triforce of Power fades and Zant snaps his neck.
More support for the theory is the fact that Ganondorf is easily killed by a blow from the Master Sword in TWW, where Ganondorf no longer posses his Triforce piece as he formed the whole Triforce.
Apart from OoT, TP and WW, there has been a game where Ganon was killed although he had the ToP: the original LoZ. The obvious difference in LoZ is that Link was wielding the Silver Arrows, suggesting that while Ganon has a Triforce piece, the Master Sword alone is not enough to actually kill him. The one contradiction against this that I can think of is LttP; Ganon does not possess a piece of the Triforce, but thee Silver Arrows are necessary to defeat him. However, seeing as he has the whole Triforce in his possession, and is in the Dark World that he created, perhaps he was more powerful than usual.
On his "death" in LttP:
I think the creators still intend for Ganon to have died in LttP. The scene with Link and the Triforce still enforces the fact that "now that Ganon has been killed, the Sacred Realm will cease being the Dark World and will become a paradise". Of course this also implies that any game featuring Ganon's Dark World or Makai cannot come after LttP, as it was gone after LttP thanks to Link. But that of course is off topic.
The problem with the one Ganondorf theory is the way that the Gerudo treat him in FSA. In OoT, the Gerudo are loyal to Ganondorf, they serve him and whatnot. However, in FSA, they are opposed to his desire for power and they neglected him as part of the tribe when he ventured into the desert in search of the Trident. This of course can be looked at as being in different eras; the Gerudo have changed between FSA and OoT, and so they do not respect this incarnation of Ganondorf for breaking their people's laws. Even so, it is unlikely that Ganondorf in FSA is the same Ganon from previous games, as his past is spoken of quite briefly. If Nintendo wanted to suggest that he was the same Ganondorf from before, I'm sure they would have made a reference to a past game.
I suppose the events of FSA are totally up to personal interpretation; I believe that FSA features a new Ganondorf following his death in WW (I place FSA on the Adult Timeline).