The retrospectives are really bad. There are two endings for OOT, you should accept this (as Aonuma confirmed in many interviews, after releasing WW, before TP and the last one in a interview in Nintendo Dream) because is the official timeline.And get your facts straight GenG. The Child Link after OoT is the same Link we see in the old school Zelda games Zelda 1 2 four swords and link to the past. The new and different Links are in the adult timeline, simply because there is no Link in that timeline after OoT.
It is mostly speculation, but that is because there isn't enough said by the developers to support the ideas. However the chronology of OoT, TP and Windwaker have been put together by an announcement from Eiji.
1) Adult ending: Ganondorf is imprisoned by Adult Link, and Zelda sends him back to his time. Time passes and the legend of the Hero of Time became old tale. Ganondorf resurrects again and Hyrule is flooded because there was no hero to stop him (no hero bloodline). The Link in WW was simply a corageous kid who was mistaken with the Hero of Time, and became the "unofficial" succesor after acquiring the Triforce of Courage. Ganondorf is defeated and Phantom Hourglass takes place.
2) After returning to his time, Link talks with Zelda about the events that were about to come. Then he went in adventures looking for Navi. In the meantime, Ganondorf was seized and about to be executed by the sages in the Arbiter's Ground, but then the Triforce of Power is bestowed upon him and breaks free. The sages doesn't stand a chance, so they sent him to the "Hyrule Junkland", aka the Twilight Realm. Then Twilight Princess takes place here.
Two different timelines.
This interview is from February:
THE WORLD A HUNDRED YEARS AFTER THE PEACE RETURNED TO HYRULE
–When does Twilight Princess take place?
Aonuma: In the world of Ocarina of Time, a hundred and something years later.
–And the Wind Waker?
Aonuma: The Wind Waker is parallel. In Ocarina of Time, Link flew seven years in time, he beat Ganon and went back to being a kid, remember? Twilight Princess takes place in the world of Ocarina of Time, a hundred and something years after the peace returned to kid Link’s time. In the last scene of Ocarina of Time, kids Link and Zelda have a little talk, and as a consequence of that talk, their relationship with Ganon takes a whole new direction. In the middle of this game [Twilight Princess], there's a scene showing Ganon's execution. It was decided that Ganon be executed because he'd do something outrageous if they left him be. That scene takes place several years after Ocarina of Time. Ganon was sent to another world and now he wants to obtain the power...
–And now we wait for the game to enjoy the rest of the story, huh? (laughs)
Aonuma: Well, that’s how things are. (laughs)
–There’s a reference to King Zora (the king of the Zora race in Ocarina of Time; his official name is Do Bon, the third), and there are some pictures of the man from the fishing pond (the owner of a fishing business near Lake Hylia in Ocarina of Time). You can get the feeling here and there that the events from Ocarina of Time happened some time ago.
Aonuma: Those things have a connection to Ocarina of Time, and we were not very sure of whether to include them or not, but the staff was having a good time, so those details just kept increasing.
–Kakariko Village and Lake Hylia haven’t changed their names, did you have in mind for their design that a hundred years had passed?
Aonuma: We clearly didn’t design Kakariko Village to reflect that a hundred years had passed. We had this town and when we decided the events that would take place there, we also decided it to be Kakariko Village, just the way it was. In this game, there are two places named, “Forest Firo-ne [Faron Woods]” and “Orudin [Eldin]”; they received their names after the three goddesses from Ocarina of Time. During Ocarina of Time, there were no such places, but after a long time, the names grew on the people living there and so those names were passed on.