This is my timeline theory. Note that I havn't played TP.
Ocarina of Time
It is said that the six sages whom sealed Ganondorf into the sacred realm was protected by the knights of Hyrule. One of them had a new-born baby. Though this is before Ganondorf's arrival, the kingdom is suffering of civil wars. In these dark times, this knight send his wife to take his son to the woods. Legends told of a child race, wich lived in the forest in peace. The parents hoped to take their son there, so he could live in harmony. Tratically, neither the wife or the son to the knight came back. However, the knight continued living in ten years, until the outbreak of a war betwen Hyrule and the Gerudo tribe. He died in the battle of Hyrule castle, wich was lost to Ganondorf, the price of theives. Seven years later, the lost son, now seventeen, apears. He is holding the Master Sword, wich was created by the gods, hidden in the Temple of Time, wich was created by the sages to prevent men to get the Triforce. This sword has the power to prevent evil. With this sword, and the help of the six sages, the last one of the knights of Hyrule defeats the evil prince, and seals him into the sacred realm. The hero was named the Hero of Time, as he had travled in time to save the world.
[Twilight Princess - have not yet played it, but suspects the game is set at this point. It can also swich place with the Minish Cap.]
Ganondorf, the king of evil, comes back, and takes over the world. To prevent total destruction, the goods flooded the world, but saved a few people. A new area is marked out in the world map - the great sea, where the kingdom once lied. Only the highest of mountaintops remain as mere islands.
The wind waker
A mysterius bird kidnaps blond girls with pointy ears, all around the great sea.
One young boy, brother to one of the kidnapped girls, sails after the bird.
He interfiers with the master of the bird, but is thrown away, and is not capable of saving his sister. However, he comes back after a while, now wearing the Master Sword. With the help of the decendant of the princess of Hyrule, he defeats the king of evil. He and the princess then dissapears to find a new land.
[Note, the new land they find is NOT the new Hyrule, and it will never be. I'll explain soon...]
The old races such as Kokiris, Gorons, Zoras is forgotten. Still, Gorons have survived the flooding, and Kokiris too... in a way.
Phantom Hourglass
_______________________________
The water has now drawn away. When the water where drawn away, many countries where made by the local people around the great sea. Still a small country in the middle of all countries apears. It is named Hyrule.
A link to the Past
The advisor to the King of Hyrule, Agahnim, makes a successful revolt against the regime. He then starts to kidnap young maidens. A young boy, wich uncle where killed by the wizard, infiltrates the castle and saves the princess. He learnes that the only way to defeat the wizard is to use the sword of evil bane, the Master Sword. When he confronts with the wizard, Agahnim sends the boy to the sacred realm. [Here is the proof the country Link and Tetra finds is NOT the new Hyrule. The sacred realm is an mirrored image of Hyrule. It lies inside of Hyrule, and even if the Hylians move Hyrule, the Sacred Realm does not.]Inside the sacred realm, the boy finds out that the wizard is acually the evil Ganon. The boy defeats the evil monster, and claims the triforce.
the Minish Cap
This is a tricky one. I really don't know where to place this one. It has to thousands of years before the Four Swords games, but the Master Sword is forgotten.
I'll update this thread tomorrow, I don't have time to continue.