Since I haven't formed much background with ALL of the Zelda games and only with the ones I have played, I came up with a rough timeline I conceived as do-able:
Ocarina of Time, then Majora's Mask (no alternate universe thing), then Twilight Princess and later on after specific catalytic events, Wind Waker and its subsequent games.
Ocarina of Time establishes our hero, however little known he is. Majora's Mask follows him as he searches for Navi (how I perceived it). With a failed attempt Link disbands his hero title altogether and lives a normal life before he starts getting too old. It starts off as denial, then he gets used to living in the shadows, then forgets he's a hero altogether. That's where Twilight Princess finds him "anew" and re-establishes him and his intentions. He remains a hero until the end of his "time" where he becomes the legend he was supposed to be, the legend that is referenced in WW where Link, the Hero of Time is reincarnated.