Minish Cap---Orcarina of Time---
Universe A: Majoras Mask ------ Links Awakening------Legend of Zelda I------ Legend of Zelda II------The Four Swords------A Link to the Past--------Oracle of Seasons
Universe B: Twilight Princess ------The Wind Waker -----Phantom HourGlass-----Oracle of Ages
this theory is all fine and dandy but i think tp should go after phantom hourglass and before oracle of ages, therefor it takes place precisely the same time as a link to the past
and as far as explaining how twilight princess goes after phantom hourglass, maybe we can simply assume that a new hyrule was created above the ocean? seem plausible to me seeing as how Nintnedo said TP takes place years and years afterwards and its the same zelda and link from ww possibly?
just a guess, havent actually played hourglass however, dont even hava ds, lol