Timeline Diagram:
Child Timeline -> MM -> TP -> LoZ -> AoL -> ALttP -> AST
Ocarina of Time
Adult Timeline -> Wind Waker -> Phantom Hourglass
Child Timeline:
Child Timeline -> MM -> TP -> LoZ -> AoL – > ALttP -> AST -> LA
Link returns to his original era at the end of Ocarina of Time (thus beginning the Child Timeline), at which point Navi leaves him. Link goes to Zelda and informs her of his departure to search for a lost friend (who could not be Epona, as Link leaves before she goes missing). Link begins his search in the Lost Woods, the part of the world which Navi originates from, but is dragged into Termina. After saving this doomed world, he and Epona (and presumably Stalkid) journey back to Hyrule, as is evidenced by the return to the Lost Woods at the end of MM, and the Lost Woods theme being played.
From Link’s return to Hyrule at the end of MM, the timeline continues, leading into Twilight Princess. TP has corresponding ruins and similar geography to the Hyrule of OoT, and the story in this game is said to occur several hundred years after Ocarina of Time. [3] Therefore we can assume that it takes place directly after Majora’s Mask.
Speculative Note: The Twilight Realm in Twilight Princess could be the same place as the World of Darkness in A Link to the Past, meaning that Link was indeed able to return there one day.
The drastically different worlds of LoZ and AoL are stated by Miyamoto to follow after OoT but before ALttP. [1]
Ocarina of Time deals with the Imprisoning War in ALttP. [2] The sequel to ALttP is the BS-X game BS Zelda – Ancient Stone Tablets, whose narrator states that “seeking new adventure, [Link] left Hyrule behind.” this journey could coincide with the ship Link journeys on at the beginning of Link’s Awakening.
Sources:
[1] Interview with Mr. Miyamoto
NP: Where do all the Zelda games fall into place when arranged chronologically by their stories?
M: Ocarina of Time is the first story, then the original Legend of Zelda, then Zelda II: The Adventure of Link, and finally A Link to the Past. It’s not very clear where Link’s Awakening fits in–it could be anytime after Ocarina of Time.
[2] “(1-6) Looks Like Ganondorf is Both Good and Bad in This Zelda“
Satoru Takizawa (Character Design):
The story in Ocarina of time isn’t actually original, it deals with the Sages’ Imprisoning War from the Super Famicom’s ALttP.
Adult Timeline:
Adult Timeline -> Wind Waker -> Phantom Hourglass
Eiji Aomura states that the timeline splits in Ocarina of Time, caused by adult Link returning to his true era via Zelda’s power, resulting in an absence of Link in the Adult Timeline. The Adult Timeline of OoT no longer has a Link, so when disaster befalls the land again, no one is there to save Hyrule (as is spoken of in the prologue of The Wind Waker). [3]
[3] Twilight Princess Wikipedia page (JP)
時代設定としては、『時のオカリナ』でガノンドロフを倒した後に、リンクが戻った時間（『オカリナ』のエンディング）から百数年後の世界という設定であり、『風のタクト』とはパラレルワールドとなっている（『時のオカリナ』で時間軸の分岐が発生して並行世界が生じているため）。
As for the timeline, Twilight Princess is set several hundred years after Link has fought Ganondorf in Ocarina of Time and returned to his own time (the OoT ending), and becomes a parallel world to The Wind Waker (the time axis originally splits in Ocarina of Time and a parallel timeline is formed).
※大人リンクがガノンドロフを封印した直後の世界の数百年後が『風のタクト』、その世界にいた大人ゼルダの 力によりリンクが元の時代に戻ってから百数年後が『トワイライトプリンセス』となる[2]。
Wind Waker begins several hundred years immediately after adult Link seals away Ganondorf, Twilight Princess occurs several hundred years after the adult Link is sent back to his original time by Zelda’s power [2].
[2] Original Source: 青沼英二インタビュー『ニンテンドードリーム』Vol.154、毎日コミュニケーションズ、2006年
[2] Original Source: Interview with Eiji Aomori in “Nintendo Dream” Vol. 154, Mainichi Communications, 2006.
Final Note:
Ultimately, the creators of the Zelda series don’t appear to have tried to impose a linear story on their games until A Link to the Past at the earliest.
A Link to the Past has an official prologue, the Sound & Drama mp3 found on the soundtrack to the game, and a semi-sequel, the spin-off BS Zelda: Ancient Stone Tablets game, but Ocarina of Time is the first Zelda game specifically stated to tie in with the story of a previous title.
Thus it seems likely that the timeline as stated by Miyamoto merely attempts to squish LoZ, AoL, and LA in to the newer story scheme, when really they were meant to be freefloating games with little relation to each other storywise (a la Final Fantasy).
Speculative Note: The AoL map contains within it a small version of the LoZ overworld map, but it’s difficult to say whether this is meant to signify anything story related (ie: the entire first Zelda game took place inside that square) or if it’s just an easter egg/visual gimmick.
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For more information about the official ALttP prologue, click here.
(Original mp3 and translation available.)
For more information about the ALttP spin-off game BS Zelda: Ancient Stone Tablets, click here.
(Original video, ROM, and translation available.)