First off, I would just like to mention that I will be refering to the Legend of Zelda a few times in this timeline theory, so if you have not heard the Legend in Zelda 2 (ironically, its revealed in the only game in the series without The Legend of Zelda in the title), go and read about it on Wiki or somewhere.
Anyways, I've been processing different timeline theories, and here is what I'm come up with:
TP playable and non-playable should line-up as well as Oracles but for some reason they didn't
LoZ refers to the game, Legend of Zelda refers to the Legend of Zelda
Ocarnia of Time
Here it splits off into 2 different timelines: the timeline where Zelda sends Link back to the past and they tell the king to stop Ganon and the one where there is no Link and just Adult Zelda with Ganon locked away. For future purposes, Young Link will be the one with Link and Adult Link will be the one without link.
Twilight Princess playable
Twilight Princess non-playable
Four Swords Adventures
A Link to the Past
Okay, so any timeline starts, and rightly so, with Minish Cap for the simple reason that Link doesn't have a cap in the beginning of that game and he does in all the rest. (side note: if you want to include more than just the games, the events of King Gustof, then the Legend of Zelda occur before the Minish Cap.)
Ah, Ocarina of Time. You revealed so much, then complicated everything. Anyways, before Minish Cap came out, Miyamoto said that OoT was the first game, so that's reason enough to put it here. But as I explained eariler, the timeline divides here. Let's move on to the Young Link Timeline, because its much easier to understand.
In this timeline, Link and Zelda have warned the King about Ganon, and a war starts. Link, wanting no part of it, heads out in search of Navi, who left him in the Temple of Time. After he saves Termina in Majora's Mask, Link tries to go back to Hyrule via the sea but gets shipwrecked (supposedly).
Wheter or not it the adventure actually happened, after you play through Link's Awakening, you battle a ghost-like figure who takes the shape of Ganon, which makes Link realize that Ganon has won the war. This leads up to LoZ. This makes perfect sense, because you have to recollect all of your items in LoZ after you lost them in Link's Awakening. In LoZ, Ganon has the Triforce of Power, and Zelda has her Triforce of Wisdom, but fearing that Ganon would steal her piece, she broke it up and hid it in 8 different places, making Link find them and then stop Ganon once more, becoming the Hero of Hyrule.
However, in LoZ, there are no castles or towns to truly speak of. This is because the Hylians moved north during the war, which is where Link travels to in Zelda 2 (Or because 8-bit processing power couldn't hold it). Here he learns the actual Legend of Zelda and discovers Hyrule again. He hunts down the Triforce of Courage and prevents the return of Ganon, then reawakes the original Zelda.
Okay now things start to get really fuzzy. The sequence after OoT seems to have happened in no more than 10 years, but we know that Wind Waker takes place 100 years after OoT in the Adult Link timeline. So, I'll be honest, I don't know exactly what point in the Young Link timeline Twilight Princess happens, but I do know that it most likely happens sometime after Zelda 2 and, in the Adult Link timeline, sometime before Wind Waker. Here's why.
In Wind Waker, it is said that there was no hero to stop Hyrule from being flooded. Sounds to me like it fits perfectly into the Adult Link part of the Timeline. The problem is, how does Twilight Princess fit into the Young Link part of the timeline?
In Twilight Princess, you get the clothes of an ancient hero. This almost has to refer to the Link in MM, Link's Awakening, LoZ, Zelda 2. Ganon comes out of the Sacred Realm to reek havoc on those who punished him. He does this at the exact same time in both timelines. Remember, in the Young Link timeline, he fought a war against the King after Zelda and Young Link warn him. But in the Adult Timeline, he is punished and locked up by the sages into the Sacred Realm. Nobody probably knows it, but he probably comes out in both timelines due to the nature of the Sacred Realm being a place of the gods and not following the laws on Earth.
So, in the Young Link timeline, Link is there and he stops Zant and Ganon. In the Adult Link timeline, there is no hero there and Zant probably floods the world out of his hatred for anything not from the Twilight Realm. Ganon decides to kill Zant and claim power for himself.
A boy named Link, who becomes dressed in the clothes of the ancient hero (Link from OoT), collects the pieces of the Triforce with help from Tetra (Zelda's descendant) and they stop Ganon together. Phantom Hourglass comes in right after this, but details are sketchy at this point because its not out yet.
Hopefully nothing radical happens in Phatom Hourglass, and the rest of the timeline can continue. A Link to The Past should occur in the Adult Link timeline due to the reference of the seven sages who sealed the great evil. However, Ganon was already freed and defeated again in the Adult Link timeline. So A Link to the Past actually occurs in the Young Link timeline. Young Link told the story of what happened in OoT to the King and it was passed down as a LEGEND, not actual truth.
We also know that the Four Swords Adventures takes place right before A Link to the Past because it was revealed that Ganon was the puppet master of Vody and he then acquires the Trident of Power. I only put this after the following events because I have no logical sequence that puts these two anywhere else except possibly after the Oracles. They could not happen directly after the Minish Cap (they have to place someplace after the Minish Cap because of Vody's prescene in the Picary sword) because the first siting of Ganon is in OoT.
Finally we have the Oracles. Their only logical place is somewhere in the future. And, because their events start out in almost the exact same way, they must be taking place at the exact same time as well. However, which one is in which timeline is still up for debate.
Anyways, hope you enjoyed my theory and hope you find some holes in it and present me with your theories. Just gotta kill time for a week or so till MP3.