Since were all talking about OoT, I just wanted to comment. My friends and I were just discussing this. All throughout Oot Link "seems" to be going back in time but in actuality he is NOT. OoT sports "reversal" of time rather then actual time travel and this is where Nintendo messes it up. Link does not travel back in time because if he did he would still be old Link when he goes back. When Link puts the sword back in he not only goes back to the past but he becomes young again. His age was reversed. Therefore any experience he had as old Link "should not" be remembered. He should not have any items to take back to the past either. When nintendo set it up so his age reverses his experience should have been reveresed also. Its actually quite a huge error in the story. BUT THEN AGAIN HE COULDNT USE THE ITEMS HE COLLECTED IN THE FUTURE IN THE PAST COULD HE. They explain away Links aging because he slept away 7 years when he originally pulled the sword and thats fine but when he travels back he should still be the same age. Either way Link should have lost the 7 years of life the sword took away from him.
I mentioned the "infinite time loop" theory in another thread and was made fun of, but if you look very closely at the end of Oot (which I just replayed) you can see clearly that Zelda is upset at the end when she turns around to face link. She is upset at what she sees in the window. It really is in fact their first meeting again. It is a time loop. It also makes sense why the hero would not show up for wind waker. In the end of Oot, Gannondorf tells them directly he is going to go after their "decendants" next time. When looking back its pretty clear that Wind Waker or a true follow up to the timeline would not have the same Link in it. I dont think Nintendo thought about a timeline until somewhere around LttP or Oot. I dont think they really cared or thought there would be so many sequels. I really dont think there is much continuity at least until OoT and WW. Even WW dosent make sense in that the hero went off to other lands... I think they were just refering to Majora's Mask. With the time reversal theory there HAS to be two realitys. One without Link in which the Hyrule he "rescued" in Oot exists, and the one where he was a kid and Majora's Mask took place. I really believe that in the end of OoT they intended the time loop theory, but then when they needed a story for Majora's Mask they just threw that away because it wouldnt make sense and it wasnt really explained all the way out in the end of OoT anyway. They leave us in the dark on purpose. So we really dont understand what happened.
As far as the original question... Link is gone, stuck in the time loop, and the legend goes on because he helped the future which the events would allow WW to take place. Leave it to Zelda to keep messing things up. She really shouldnt have the triforce of Wisdom because she shows nothing of the sort. She keeps getting kidnapped, and now she got Link in an infinite bind. Its funny in WW how Gannondorf just keeps tossing her aside like shes nothing. But then again I suppose Corruption would always just toss wisdom to the side.