I believe that Ocarina of Time was intended to be the first Zelda story, with the followup Majora's Mask featuring the same Link. Then next in the chronology were A Link to the Past and Link's Awakening respectively. I base that primarily on the fact that the story of Ganondorf was already known by characters in the game. The NES Zeldas would have to take place further in the future, because the villages in Adventure of Link had the same names as the sages in OOT (A neat bit of retroactive continuity
). And of course, Wind Waker has to take place last. The Oracle games could technically fit in anywhere after Majora's Mask (Link looks a little more teenaged). So, as I see it:
Ocarina of Time
Majora's Mask
(Oracle Games?)
A Link to the Past
Link's Awakening
The Legend of Zelda
The Adventure of Link
Wind Waker