The Legend of Zelda series have been a great and hard puzzle to solve, the timeline until now is unknown, but Shigeru Miyamoto already stated that the timeline was made before starting the series, so this means there is a specific timeline to follow and today I will talk mainly about the order of the games and why they are first or the very end in the timeline. Remember this is made by me, and my thoughts on the timeline, I will try to specify as most as possible and I'm not saying this is the correct timeline.
The Legend of Zelda Skyward Sword: This game is the starting of the series, first off because the Master Sword wasn't still created instead we have the Goddess Sword (which is then turned into the Master Sword) another thing is that at the videogame´s back box it says: "The Birth of the Legend" which in other words means that this is the starting of everything, another fact could be the planet wasn't still discovered, and there are no humans in the earth, also mentioning that the civilization in Hyrule does not have enough technology (like in Skyloft).
The Legend of Zelda The Minish Cap: In the introduction cutscene of The Minish Cap it says: "A Picori appeared from the sky" that means Link from Skyward Sword which came from Skyloft and reached the planet. Also the civilization is still the same as the one in Skyward Sword! But now humans are habitating the whole world. The Master Sword still is not present in this game, instead we have the Picori Blade which is the "important" and main sword in the game.
The Legend of Zelda Four Swords: This game is connected with the Minish Cap, as well there are not much technology, but this time the same Link picks up the "Four Sword" (in other words the upgraded Picori Blade) and this multiplies Link by four! then he continues his journey and re-battle the main villian from The Minish Cap called Vaati and finally kills him.
The Legend of Zelda Four Swords Adventures: The game has basicly the same mechanics as Four Swords but now for the first time a new enemy appears called "Ganon" (the pig) which is defeated by Link and his multiple clones! Then the Four Sword is putted back to the pedestal and finally the story ends, Shigeru Miyamoto said that The Minish Cap, Four Swords and Four Swords adventures were before Ocarina of Time in which I will talk about right now!
The Legend of Zelda Ocarina of Time: This game is the most important part in the timeline because it messes it completely up! First off, it splits the timeline into 2 parts which are called the Child timeline and the Adult timeline. I will talk about them later as we progress, but now let´s talk about why is Ocarina of Time in this place. As the Master Sword is already created in this game we surely know that Ocarina of Time is after these four games, even though Shigeru Miyamoto also said that only three games were before Ocarina of Time and that they are The Minish Cap, Four Swords and Four Swords Adventures, as we have a clue that Skyward Sword is before the Minish Cap I think we need to say they are four games before Ocarina of Time, and also Link opens the Gate of Time (in which was closed in Skyward Sword) which means it was the first time they opened the door to get the Master Sword so at this point and so far we are correct in the timeline!
NOTE: As I told you, the timeline will now be divided in 2 parts called "Child Timeline" and "Adult Timeline", each of them has different games. Ocarina of Time split the timeline because as you saw Link did go to the future leaving behind his parallel world, then Zelda sends Adult Link (with the Ocarina of Time) back to his parallel world, but Zelda still continues her life so they exits two parallel worlds (Child timeline and Adult timeline in this case)!
Want to see the other two parts of the timeline? Be sure to check them out:
Child Timeline: NOT DONE
Adult Timeline: NOT DONE