Minish Cap has to happen before Four Swords. The sword in it eventually turns into the Four Sword. I actually came up with a timeline that I've yet to find any plot-breaking contradictions in.
Minish Cap comes first, because Link first receives his hat in this one. This is important because the Minish would later evolve into the Kokiri, which is why they would wear the green clothes and hat. There are also no references to Ganon as of yet.
Afterwards, Vaati breaks the seal on the Four Sword and kidnaps Zelda in The Four Swords. A new Link rescues her and imprisons Vaati again. That's when Four Swords Adventures happens, in which Ganon creates Dark Links to trick Link into unleashing Vaati. Link kills Vaati and imprisons Ganon within the Four Sword.
In OOT, a new Ganondorf arises. His backstory is different from the one in Four Swords Adventures, so it's likely that they're different characters, much like how most games have a different Link and Zelda. One Dark Link from Four Swords Adventures had become a minion of Ganondorf. The events of OOT happen and a split in the timeline is caused by Zelda sending Link back in time. On the child side of the timeline, it goes straight to Majora's Mask, a direct sequel to OOT. Twilight Princess happens after Majora's Mask, which has been officially confirmed.
A Link to the Past must take place after Twilight Princess on the timeline, because, sometime between Majora's Mask and Twilight Princess, something happened that caused the Master Sword to be moved to the Sacred Grove. In this, Ganon still has the Triforce of Power and finally managed to take the Triforce of Wisdom from Zelda. Thus, when Link defeated Ganon at the end, he was able to obtain all three pieces of the Triforce and complete it.
Starring the same Link, the next games in the series are Oracle of Ages and Oracle of Seasons, in either order. Following the end of A Link to the Past, it shows the completed Triforce at the beginning. After defeating secret final boss Ganon, Link tries to take a boat back to Hyrule- But gets caught in a storm and washes up on an island. This is the next game, Link's Awakening. This is most definitely the same Link from ALTTP and OOA/OOS, because the nightmare takes the form of Agahnim and he starts off on the same boat from OOA/OOS.
Much later, the Triforce is split into three pieces once again. The Triforce of Wisdom was split into many pieces and hidden throughout southern Hyrule. The Triforce of Courage was split into many pieces and hidden throughout Northern Hyrule. A new Zelda kept hold of the Triforce of Power, fearing it would fall into the wrong hands. This leads up to Zelda I, where Ganon returns and reclaims the Triforce of Power. Link has to find the Triforce of Wisdom in order to fight him and save Zelda.
After the events of Zelda I, of course, come Zelda II. The same Link from Zelda I has to wake up the original Princess Zelda, who was put to sleep a long time ago. To do this, he has to find the final piece of the Triforce and put it back together to wish Zelda awake again. After defeating the (probably) final Dark Link, Link finds the rest of the Triforce and saves Zelda.
On the other side of the timeline, in which there is no Link, Ganondorf breaks free and tries to take control of Hyrule once again. Because of this, the Goddesses give Ganondorf what he wants- By flooding Hyrule and leaving everything in it, except any life forms, to Ganondorf and his Moblins. As a result, Ganondorf finds a way to break out, leading to the events in Wind Waker. At the end of Wind Waker, Link and Tetra go off to discover a new Hyrule, in Phantom Hourglass. During this time, they find themselves transported to the same world that was in Link's Awakening.
Finally, Link and Tetra discover a new land and name it Hyrule. Link works with some of Tetra's crew, while Tetra herself becomes the queen. Three generations later, the only member of Tetra's original crew remaining is Nico. This game, Spirit Tracks, stars the grandson of the Link from Wind Waker and the granddaughter of the Zelda/Tetra from Wind Waker.
Feel free to try and tear this one apart with theories. But I've found fewer contradictions in it than any other timeline I've come up with (and I've come up with a lot).