Well, it's hard to say. Every Zelda game with Ganon being the ultimate, final boss, it seems like he dies. The End. The Wind Waker, with the sword being thrust into the skull and Ganon subsequently being turned into stone, I think, is just another way for him to die, but some may argue that Nintendo had made it more "dramatic", so to speak.
both TP and WW show Ganondorf actually dying. if you notice, every game that goes after those games on a timeline only has Ganon, not Ganondorf. its safe to say that TP and WW is the end of Ganondorf but its also possible for Ganon to be revived and that seems pretty obvious that that is what happens.