There are a huge amount of timeline theories that have been put out there by the fans.
The developers, namely Aunoma and Miyamoto, have confirmed that the split in the timeline does exist. Ocarina of Time's ending splits the timeline into two: the Hyrule just liberated from Ganondorf, and the Hyrule seven years in the past. They are referred to as the Adult Timeline, since the Hero of Time was an adult in that era, and the Child Timeline, both respectively.
Majora's Mask occurs in the Child Timeline, as the young Link just sent back into the past embarks on a journey to find a long-lost friend, presumably Navi.
Windwaker occurs on the Adult Timeline, for two reasons:
1. Ganondorf is sealed in the Sacred Realm only within the Adult Timeline. In the Child Timeline, he is still at large, though that is dealt with soon (I'll explain later). The prologue of WW mentions Ganondorf as the one who broke free from the Sacred Realm.
2. Despite the plight of the Hylian people, the Hero of Time does not reappear, as mentioned in the prologue of WW. This is because he no longer exists within the AT, as he had returned, many centuries ago, to relive his childhood and embark on the journey in Majora's Mask. He is forever gone from that paradoxical dimension that is the Adult Timeline.
Twilight Princess occurs in the Child Timeline, as confirmed by the developers. While there isn't much proof, there isn't much proof to say otherwise. However, if you look at one part of the plot it does make sense:
Remember the ending of OOT? The final, absolute, real ending? The one with a young Link meeting Zelda in the courtyard? My theory is that Link was there to warn Zelda about Ganondorf, who she would have already suspected as a villian at the time. Link did not make the same mistake as he did before (which finding the three spiritual stones and essentially lure Ganondorf to the Sacred Realm), but instead bid farewell to Zelda and head to to find Navi. Later on, Ganondorf was caught committing a serious crime, put on trial, and sentenced to death. During the execution, though, Ganondorf survived through a "divine prank" in which he somehow obtained the Triforce of Power and broke free, killing the Water Sage. The other Sages quickly activated the Mirror of Twilight and banished him to the Twilight Realm.
Phantom Hourglass and Spirit Tracks are sequels to Windwaker. (Confirmed)
Skyward Sword is a prequel to Ocarina of Time. (Confirmed)
Based on all of that, this is the timeline so far: (Abbreviation go according to first letters of the title, for ex. Ocarina of Time: OOT, Majora's Mask: MM, Windwaker: WW...and so on)
(Adult Timeline): ---(Hundreds of years later)----WW->PH--(100 yrs later)-->ST
SS--(Unconfirmed time length)--OOT
(Child Timeline) ->MM--(100 yrs later)-->TP
Unforunately, the placements of A Link to the Past, Four Swords Adventures, Link's Awakening, and others are debated even today.