The way I see things working is this: you have 2 timelines, the split occurring when Zelda sent Link back in time and the end of Ocarina of Time. Wind Waker is the end of the timeline that follows from the end of the "Imprisoning War". eventually Ganon reappeared, and Hyrule was flooded. centuries passed, life went on on the islands that were created and tada WW.
Majora's Mask follows shortly after the end of Ocarina in the other Timeline, and ALTTP continues this thread. It can't have happened before WW because the Triforce is whole, and it can't have happened after because in the last moments of WW, Hyrule was destroyed and the King drowned with his wish on the entire Triforce. "the world above" was clearly NOT Hyrule, and a "new Hyrule" that Link and Tetra set out to find would not have been as connected to the lore and history of the first Hyrule as was the Hyrule of ALTTP. Which means ALTTP belongs in the MM timeline. Also, WW states that the Hero of Time did not return, which would seem to indicate that none of the games occured in this time period.
Now, the other games would seem to fit on this timeline too, depending on what state the Triforce is in. I could believe that Link's Awakening goes in the WW timeline, perhaps occurring after Link left to find the new Hyrule, but I have also heard a good case for EVERY SECOND of L'sA occuring in a dream during the seven years where Link was inprisoned in the Sacred Realm. I'm sorry I can't give anything more than that, but I haven't played many of the early games, or the Oracle games.
this theory has AT LEAST 3 Links: OoT-MM, WW-LA and ALTTP. OR LA before end of OoT followed by MM, WW Link2, ALTTP Link3. Depending where you place the other games, there are probably more.
So that's my 2 cents.