Nintendo made it official that Ocarina of Time is chronologically the first in the timeline, and from it, we have two timelines due to the time paradox created by the Link and Zelda of that time, whom I'll be referring to as the Hero of Time and Princess of Wisdom.
Child Timeline: The Princess of Wisdom not-so-wisely returns herself and the Hero of Time back to when they were both kids. Navi leaves, the Hero of Time warns the Princess of Wisdom about what Ganondorf is planning, then takes the Ocarina of Time and leaves for Termina (though he doesn't know Termina is his destination yet). Searching for Navi, the Skull Kid he befriended during his prior adventure, now possessed by Majora's Mask, steals the Ocarina of Time and the pony Epona, which causes the Hero of Time to give chase and end up being transformed into a Deku Scrub. Using his limited power in this form, he steals the Ocarina of Time back from the masked Skull Kid and plays the Song of Time to rewind time by 3 days, and relives those 3 days over and over again to take the Remains Masks from the north, south, west, and east corners of Termina, while also solving other problems, like he did in his prior adventure. Letting himself be swallowed by the possessed moon, he defeats and recaptures Majora's Mask, then sets off to look for Navi again. We don't hear of him after that.
Many centuries later, the Hero of Twilight hears from the Sages that Ganondorf committed some huge atrocity and was sealed up in the Twilight Realm for it. The Hero of Twilight, with Princess Midna's help, kills Ganondorf by stabbing him through the heart. This act causes Ganondorf to lose the Triforce of Power, most likely to the Hero of Twilight.
Adult Timeline: The Hero of Time, wielding the fabled Master Sword, comes out of nowhere and awakens the six Sages, then moves on to defeat Ganondorf. He succeeds, and the Sages and Princess of Wisdom seal him up in the Evil Realm, where the Triforce once slept.
Many centuries later, a legend is passed down about the adult Hero of Time, who vanished after defeating Ganondorf. Ganondorf reappeared, took over Hyrule, and then found it to be a gigantic swimming pool overnight, due to the Goddesses flooding it so badly that it ended up the Great Sea. A young female pirate by the name of Tetra (who is later revealed to be Princess Zelda reincarnated) takes the Hero of Winds (poot poot fart stinky just kidding maybe) from Outset Island, dressed in similar clothes to the Hero of Time, to try and save his sister, Aryll. He fails, and ends up embarking on a huge journey to reclaim the Triforce of Courage and defeat Ganondorf. He succeeds, Ganondorf turns to stone, the unified Triforce is sent to sleep at the bottom of the sea, and peace is restored. Later, the Hero of Winds travels with Tetra to a new area of the Great Sea, where Bellum is causing havoc. Tetra is captured and turned to stone, and the Hero of Winds teams up with Linebeck to rescue her and kill Bellum. He succeeds, and the Ocean King restores Tetra.
These are the concrete ones we know. Where the rest fit in, I'm not sure. However, I think I can shed some light on which timeline some of the other games occur in.
First and foremost, keep in mind that there is only one Ganondorf. The only reason we see two here is because of the split timelines. Link and Zelda had descendants; Ganondorf just kept coming back from being sealed away. However, he could only do that as long as he held the Triforce of Power. He lost that after the Hero of Twilight killed him, so there's probably only one or two Heroes who come after the Hero of Twilight in that timeline.
The Hero of Seasons and Ages had two lands to deal with, and if you linked the games, you'd know that the Zelda of the time was captured by Twinrova, who we know to be Ganondorf's surrogate mother. Twinrova sacrifices herself to bring Ganon back. She mentions that she's going to call forth Ganon's spirit, which means that this adventure takes place in a timeline after Ganondorf has been killed. That means this is the only one that happens after the Hero of Twilight wipes out Ganondorf. It would appear that the Hero of Seasons and Ages is a little younger during his adventure than the Hero of Twilight was. My guess is that this adventure took place a few centuries after the Hero of Twilight's adventure. Twinrova most likely hid behind the scenes, studying up on how to create the Flames of Destruction, Sorrow, and Despair needed for the dark ritual that would revive Ganon. Considering the lack of the Triforce of Power, I'd imagine that Ganon, not Ganondorf, returned due to the energy put into the dark ritual. It took a lot of power to create those flames; look at everything Veran and Knox did, the power they had, and then their defeat. That just left the final flame.
The Hero of Dreams, who traveled to Koholint Island (The Legend of Zelda: Link's Adventure), cannot be put into a timeline with only the information we have. All we know is that he was sailing at sea somewhere, he was an adult, and he was knocked out by the storm. Considering he had to wake the Wind Fish, we can somewhat safely assume that this was the original Hero of Winds, whom I've already mentioned, several years after his adventures with Linebeck and the Ocean King. That's just a guess, though. If it's correct, though, it would leave open the question of why and how the Hero of Winds was separated from Tetra.
It's clear that the same Hero who saved the Zelda of his time in The Legend of Zelda was also the star of Zelda II: The Adventure of Link. I'll call him the Hero of Hyrule, since nothing else really gives him away. Now, the games make it clear that the original Princess Zelda was involved, which means that it's the same Princess of Wisdom as before. However, it's also clear that these particular adventures took place long after the Hero of Time's time. Considering that Ganon is the game's final boss, and the Triforce of Courage isn't even mentioned once, it's clear that this adventure takes place in the Adult Timeline. Remember, Ganondorf had broken his seal, and still had the Triforce of Power. However, the legend states that the Goddesses flooded the world, so Hyrule was no more and we got stuck with the Great Sea. That means somehow the Great Sea was drained. Thinking of the nonfiction tale of Noah's ark, that's not exactly out of the ordinary. I imagine that the Great Sea was simply drained naturally, leaving Hyrule behind. However, having all that water there would have changed the geography of Hyrule through erosion and such. The people had to rebuild, and most likely Tetra was a part of that. If my guess on the Hero of Dreams is correct, it would explain why they were separated. The Hero of Winds would most likely find a small home somewhere and settle down. Tetra would claim her throne as Princess Zelda, and peace would reign for a while. And then Ganondorf tries coming back again. Remember, the Triforce splits when Ganondorf touches it, so he most likely was able to reclaim the Triforce of Power, and the Triforce of Wisdom and Triforce of Courage went to the most deserving candidates. Obviously, that would be the Link and Zelda of the time, to keep the epic triangle intact. However, since the Hero of Hyrule had to reclaim the Triforce of Wisdom in eight shards, most likely Ganon, permanently transformed by a combination of his madness and the sheer power needed to break him out of his stone prison, captured Zelda quickly and ripped the Triforce of Wisdom from her. Without any Sages to lock him away again, the Hero of Hyrule had to fight alone, but this time with two Triforce pieces within him. Also, considering even the Hero of Time couldn't kill Ganon, it's most likely that the Hero of Hyrule couldn't, either. Most likely, Ganon was just defeated, and he had no choice but to wait until a dark ritual could be held to strengthen him again, since he lost the Triforce of Power. However, unlike Twinrova's ritual with the three flames, the blood of the Hero was required for this one. I would imagine that this is why the Dark Mirror was created by Ganon, his minions, or a combined effort. The Hero of Time would pass by it, and Dark Link would be created. Disguised, Dark Link would try to persuade Zelda to help with getting the Hero's blood, but be unable to, and thus put her to sleep. The Hero of Hyrule would then have to go on another journey to defeat Dark Link and wake Zelda up. In other words, Ganon foresaw the possibility of his defeat. Now, remember the events of Ocarina of Time, and the legend told on Outset Island later in Wind Waker. Ganondorf rose again, but there was no Hero to vanquish him again, so the Goddesses flooded the world. In the time period before the flood but after Ganondorf's return, it is likely that Ganondorf created the Dark Mirror in this time. Dark Link was created, and Zelda was put to sleep. She was kept safe in a glass sarcophagus, until a Hero would awaken her. This sarcophagus would be lost at the bottom of the sea, kept safe in one of Hyrule Castle's towers, until the Great Sea drained naturally, and the Hero of Hyrule vanquished Ganon. Why, then, is Zelda clearly awake during the first of these two games? Because Zelda II occurs BEFORE Legend of Zelda. It was only called Zelda II because it was the second game made. Also, remember that people had to move back into Hyrule. It would make sense, therefore, for all those little villages being there, and Death Mountain being on the south side of your map. The people were migrating towards Death Mountain, so that the Kingdom of Hyrule could be rebuilt where it was, but they had to get there first. Most likely, even though Link beat Dark Link and woke Zelda up, Ganon's minions still got some of his blood, so he had to go defeat Ganon, rescue Zelda, etc. anyway. Honestly, it wouldn't be that hard to do, especially if Dark Link was created for getting that blood anyway (and he was). No Hero would escape that battle unscathed.
We can't really pinpoint when Four Swords and Four Swords Adventures take place, either, since the main enemy is Vaati. Ganon appears as the final boss in FSA, yes, so we can use that. Clearly, Ganon is able to speak intelligently, and not just chant, "KILL! KILL! KILL!" Therefore, this is the real Ganon, and not a terrible replica, like Twinrova ended up with against the Hero of Seasons and Ages. In these games, Vaati was already sealed inside the Four Sword, but was able to escape, capture Zelda, and have the Hero of Four go on his adventure. Vaati was also already in his huge black eye form, which means his power as a wind mage was already fully realized. As such, we can say that both of these games take place before The Minish Cap. As far as Four Swords Adventures goes, Ganon just realized that Vaati was causing havoc, and decided to take advantage of that by using it as a smokescreen for his plans. Now, this adventure involves Shadow Link, whom I just think is a renamed Dark Link. There's really no difference between them; both came from the Dark Mirror, etc. However, thinking back to the Water Temple explored by the Hero of Time, we can call that the true Dark Link. That means that the "Dark Link" from Zelda II: The Adventure of Link was actually Shadow Link. Anyway, I'd imagine that the same Hero of Four had to deal with Vaati in both games, so there's really nothing left to glean here. As far as when this adventure occurs, since Ganon and Shadow Link are around in the second adventure, I'd say it happens a couple centuries or so after The Legend of Zelda. How Ganon comes back again is unclear, but most likely he just had some of the Hero of Hyrule's blood leftover from the first ritual. This time, however, he decided to bide his time and work from the shadows, rather than just jumping into action again.
In The Legend of Zelda: The Minish Cap, we learn about Vaati's origins as a member of the Minish. We also get to meet the Oracles Din, Nayru, and Farore. Obviously, this adventure happens a few years after the Hero of Seasons and Ages defeats Ganon. However, it's also obvious that this is a different Hero, so we'll say it was the Hero of Four, because he's the one who originally had the Four Sword created/awakened. Why Vaati was sealed in the Four Sword isn't made clear here, however, so we will have to assume that Vaati went back to his dark intentions, and we get The Legend of Zelda: Four Swords as a result. Remember, Zelda had the Hero of Four meet her at the Four Sword's shrine? She said that "you already know about Vaati."
That should leave only The Legend of Zelda: A Link to the Past. Here, we meet the Hero of Twin Worlds, who actually went into the Evil Realm, or Dark World as it was called in the game, to defeat Ganon. Obviously, this game occurs in the Adult Timeline, because Ganon is still sealed in the Evil Realm. I'd imagine that this adventure took place before Ganon's return to Hyrule, but not by much, since Ganon was able to create Agahnim and send him into Hyrule.
So yeah, that should help clear things up.
