Spoiler:
When Zelda sends Link back in time at the end of OoT, it causes a split in the timeline. This should have been immediately noticeable.. People all over Hyrule are celebrating Ganondorf's defeat, but if Link had changed the past, it would have been instantaneous and there would be no defeat to celebrate.

Anyway, one timeline (Timeline 1) continues along after Ganondorf's defeat. One hundred years later, he returns and there's no Link to fight him. Blah blah blah, the world gets flooded, etc. All that stuff from Wind Waker.

The other timeline (Timeline 2) is what we see at the very end of OoT, with Link returning to the past. There is an oddity here, as Link arrives on the Pedestal of Time, which was not accessible until after Zelda had fled, yet Zelda is still in the garden. Anyway, since Zelda was in the garden looking in that window, we can assume he arrived at the time when they first met. Knowing everything that happened the first time, Link would not recollect the spiritual stones. I'm sure he'd defeat King Dodongo and save Princess Ruto again, but he wouldn't collect the stones, and he wouldn't let Ganondorf into the Sacred Realm.

Sometime shortly after his return (a year at most) he accidentally goes on his adventure in Termina. Nothing major happens here, but we know it's right after OoT.

Now, you're probably wondering why I placed Minish Cap and the Four Sword games where I did. That all boils down to two things. First, Ocarina of Time has been official stated as occurring first, so none of the MC/FS games can be before it. Second, in FSA we see the Dark World and Pig Ganon. Now, the Dark World was created during the time of The Imprisoning War, when Ganondorf obtained the Triforce, causing the Sacred Realm to mutate based on the dark wishes of his heart. This is also what turned Ganondorf into Ganon. But when Link gets the Triforce at the end of LttP, the Sacred Realm is (presumably) returned to normal, and all that were trapped there are returned to the normal world (as seen in the credits). So in order for these things to be present in FSA, it'd have to be set between The Imprisoning War (which would be after MM, since Ganondorf isn't immortal until he gets the Triforce (or at least the Triforce of Power, as seen in the other Timeline)) and LttP. Anyway, moving on..

Now, as for why I place the Oracle games between LttP and LA, Link was returning to Hyrule from a far-away land by ship in LA. When you beat both Oracle games (using one's password when starting the other) the ending clearly shows Link leaving Holodrum/Labrynna by ship. Also, Aghanim appears in the Oracle games.

The Time of Chaos between LA and LoZ need some explaining... Not much information on it from the games. I'm pretty certain "Time of Chaos" is a fan-term, for that matter. In any case, it refers to events that we know happened. It is during this time that a King of Hyrule hid the Triforce of Courage in the Valley of Death. His son, the Prince, was power hungry, and being influenced by a dark sorcerer (possibly Aghanim). So when he (the King) died, he told only his young daughter, Princess Zelda, where the Triforce of Courage was. The Prince tried to get his sister to tell him, but she refused. So the sorcerer put a spell on Princess Zelda, causing her to fall into a deep sleep from which she might never awaken. Some time after all this, something happened led to Hyrule breaking up into several smaller countries, only one of which would retain the name Hyrule.

Then, of course, there's the Legend of Zelda and Zelda 2.