I refined my time-line. Remember some of this is speculation.
I assume that Hyrule was not originally inhabited by the Hylians. I think the Picori, the Wind Tribe, and the Sheikah were the first natives to the land. I also think that Hyrule Castle was not build by the Hylians, but a more ancient race that died out before the Hylians came. I also think the Wind Fish lived around Hyrule for a time.
During the Hylian colonization, or shortly thereafter, Link the Great and Zelda the Fair sealed the monsters of Hyrule into the Picori Sword with the help of the Sacred Light. I call them “Link the Great” and “Zelda the Fair” because they resemble the two, but are not featured in any game (yet).
“The Minish Cap”
I think this game occurred only a hundred years or so after the colonization of Hyrule. I say that because the population in Hyrule is quite low, when there are no monsters around to kill people. There are also few structures, indicating early iron age technology. There is also no “Death Mountain”, like in other Zelda games, and the monsters abundant in other games are released in this one. Gorons are implied to be coming from a distant land, and the Zoras are absent all together. To cap it off, the cap in the “hero’s garb” is included at the end of this game.
“Four Sword”
Not to long after “The Minish Cap”, chaos breaks out in Hyrule. Link I pulls out the Four Sword to help, but frees Vaati in the process. Vaati kidnaps Zelda I and Link I saves her. I think the maps in this game are mostly outside the boarders of the map in “The Minish Cap”.
After the events of "Four Sword", I think Link I and Zelda I married, making every Link and Zelda thereafter distantly related. Some time after they die Veil Falls erupts and is renamed “Death Mountain”. Zoras appear in what is called “Zora’s Domain”. Zora’s River opens and creates a new Lake Hylia over the Castor Wilds and the Wind Ruins. Hyrule Town becomes Castle Town and Kakariko Village is built. “Minish Forest” is renamed “Lost Woods”. The Gerudo make contact with Hyrule.
“Ocarina of Time”
I think this game occurred about 150 years after “The Minish Cap”. Link II and Zelda II are probably third or fourth cousins, and both unaware of it. Apparently the Gorons and Zoras have colonized Hyrule completely and have a well-rooted culture.
The end of the game implies a split time-line. The end of the game doesn’t agree with the back story of “Link to the Past”, which says that many knights protected the sages.
Adult Time-Line
“The Wind Waker” & “Phantom Hourglass”
Hundreds of years after “Ocarina of Time”, Ganon returns and the world floods. Later Wind Waker Link and Tetra have their adventure to save the Triforce. The Triforce comes to the possession of king, Daphnes Nohansen Hyrule comes to have the Triforce. “Phantom Hourglass” happens a year or so afterwards.
Standard Time-Line
“Majora’s Mask”
After Zelda II sent Link II back to the past, Link went back to Zelda and they tried to sever Ganon from Hyrule. Link eventually goes out in search of Navi, resulting in the adventure in this game.
The Seal War described in “Link to the Past” and “Twilight Princess” probably come to pass shortly after Zelda II sent Link II back in time (five years, I’d say). The Knights of Hyrule, perhaps Link with them, defended the sages as they sealed Ganon. However, Ganon managed to kill one of the sages before the seal was complete and went to the Twilight Realm, but was still trapped. As for which sage died, I lean towards Rauru; but Darunia seems the more logical possibility. After the war, I presume that Link II married Malon.
Over the next few hundred years, deforestation goes up, expanding Hyrule. There is also an obvious population growth. Zora’s Domain dries up and the Zoras move to a new “Domain”. Hyrule is divided into the four territories. This is the Golden Age of Hyrule, as seen in “Twilight Princess”.
“Twilight Princess”
Several hundred years after “Ocarina of Time” (I’d say about 600), Ganon escapes from the Twilight Realm. Note that Link III and Zelda III seem to be the only ones that know about Ganon’s involvement, thus it is unmentioned in the legend told in “Link to the Past”. The question is, how did Link III complete the seal? I suspect that Malon is, in fact Rauru granddaughter, thus Link III has a fraction of Ruaru’s sage-powers. Not much, but enough to finish the seal. I think Link III married Ilia, who I think is descended from Saria.
Fifty years or so after “Twilight Princess”, Ganon regains lost pieces of Triforce, but remains sealed. An earthquake (probably caused by him) causes Death Mountain to collapse, destroying the original Hyrule Castle, and redirects Zora’s River making a new Lake Hylia that drowns out many of the southern and eastern cities. Ironically, a desert forms where Lake Hylia once was. Castle Town is modified into a new Castle and a new Kakariko Village is built. The plummet in the population allows the forests to grow large again.
“Link to the Past”
A few hundred years after “Twilight Princess”, Agahnim comes to “aid” Hyrule. He takes control and opens up the door for Ganon to return. Link IV, of course, impedes this act and eventually defeats Ganon and takes the Triforce.
“Four Swords Adventure”
Shortly after the events of “Link to the Past”, Ganon recovers from the serious injury Link IV gave him and eventually meets Vaati. The two work together to achieve their comon goal. Ganon seeks out a Trident he replicated with the Triforce in “Link to the Past”, believing that if he becomes strong enough he can take the Triforce away from Link. Link, once again,
stops him, killing him this time.
I think Link IV married Zelda IV and became the next king of Hyrule. They had two children, a son and a daughter. They named the daughter after her mother, who was identical to her. One of the six maidens in the previous two games, Impa II, serves the Princess Zelda IV.
“Oracle of Ages” & “Oracle of Seasons”
Around the time Link IV dies, Link V visits the shrine of the Triforce. It is possible he is allowed entrance because of the birthmark on the back of his hand. The Triforce transports him to the lands where these games occur. At the end, Twinrova sacrifice themselves to revive Ganon. However, because they had impure souls, Ganon is only a monster. Link V saves Zelda V from him and kills him.
“Link’s Awakening”
After his two adventures, Link V sails to parts unknown. He is shipwrecked and taken to the Wind Fish’s dream. He wakes the Wind Fish then makes his way back to Hyrule.
During the events of “Link’s Awakening”, the brother of Zelda V seeks the Triforce under the corruption of a sorcerer (I’m assuming it’s Agahnim). Agahnim puts Zelda in a irreversible sleep when she doesn’t cooperate, revealing that he wanted the Triforce for himself. I think Link V eventually returned and helped the Prince get rit of Agahnim.
Hyrule begins flooding (probably fifty years after “Link’s Awakening”). Hylians inhabit South Mountain, but all die. The mountain is renamed “Death Mountain”. It turns out the mountain was inhabited by Ganon, who was revived by Agahnim.
“Legend of Zelda”
A hundred years or more after “Link’s Awakening”, Link VI goes to Southern Hyrule and meets up with Impa III. She tells him that Zelda VI has been captured by Ganon, who is looking for the pieces of the Triforce of Wisdom. Link saves Zelda and slays Ganon. This time, Ganon is dead for good, maybe...
“The Adventure of Link”
Not long after “Legend of Zelda”, one or two years, Link VI learns that he is destined to obtain the Triforce. Nothing to add to that.
That took a long time. Hope that settles a few questions