WIND WAKER SPOILERS!!
LoZ and AoL take place last on the timeline (unless you place the Oracles after them).
In response to Ocarina's question, I'm not quite sure at which point Ganondorf can no longer transform at will, but he obviously can in at least OoT and WW. In Ocarina of Time the Triforce splits when he touches it and he is left with the Triforce of Power. This allowed him to change into Ganon after you defeated him when he was Ganondorf. You'll notice, however, that he was sealed away as Ganondorf. In Wind Waker he starts out as Ganondorf as well, then changes to Ganon, then back to Ganondorf when you finally defeat him. By LttP, though, it is clear that he can only be Ganon.