Let me start by sying that this is by no means definitve, or canon for that matter. Most of this is guess work, aided by "hints" and a few defininte canonical links. One thing right off the mark-Ivalice and Vanadiel will not be mentioned-they have too unique mythologies to tie in with the other ten games.

Note:For each individual games, I will use the terms BC and CC for specific dates in that timeline-BC or Before Crisis for dates leading up to the start of the game, and CC or Crisis Core for dates during the game(athough this is generally not used often)

The story starts with two separate worlds, which I'll call Terra and Gaia.
The world of Final fantasy 1 is Terra, and FF2 takes place in Gaia.

--Terra--
The first thing is, of course, the creation of Terra. In the Void, the four elements came together, forming a world of Light and the crystals. A second "shadow world" called the World of Darkness was also made at this time, on the opposite side of the Void, with it's own set of Dark crystals. At some point, there was a first imbalance of light and darkness, with light infringing on the world of darkness, summoning the Cloud of Darkness, which was defeated by the Warriors of Darkness (Note: the timing of this is unclear, as is whether or not they were aided by warriors of Light)
-FF1-
2000+BC: The temple of Fiends built at the centre of the world map by unknown hands, presumably for worship of Chaos
2000BC: Garland is returned to this point by Chaos. The Four fiends, seemingly avatars of Chaos like Garland, are sent into the future. since, when the party return to this time they encounter the fiends at the foot of staircases, the fiends were either orignally intended to wreak havoc in their present, or had to leave the temple to travel forwards in time, following the same path as the Heroes.
The Warriors of Light are defeated by chaos, and the fiends are sent forwards in time. Also, the Warriors of Light defeat Chaos, and time begins to flow again, normally. The world may have experinced vast changes at this point, since the flow of normal time has been held back an unknown number of years, each cycle lasting 2000 years.
400BC: Tiamat drive the Lufenian people from the Floating Fortress, and blocks the flow of energy from the Wind Crystal. The wind stops.
200BC:Kraken appears and drives out the Merfolk of the Sea Shrine, which is then sunk.
<1BC:Lich and Marilith appear in melmond and Gulug volcano respectively. Lich darkens the earth crystal and the earth around melmond becomes barren. Marilith burns all in her wake as she darkens the fire crystal.
CC:The game begins. The Light warriors defeat garland at the ruined temple, afterwhich he travels back 2000 years. They recieve the lute from Sara. The Warriors restore the crystals with the shards they hold, defeating the four fiends. They return to the teample, and travel back in time, using the Lute to chase after Chaos. They defeat chaos, after the story has cycled an unknown number of times, and return to the fiendless present, Wher Garland awaits.
Unknown Time:the Soul of Chaos dungeons may be either fragments of the world as it should have been without chaos, or fragments of the World of Darkness(in FF3, it is only seen as a few areas, connected by telporters, much like soul of Chaos.)
Conjecture-After FF1: Just as Ganondorf was stopped by young Link at the end of Ocarina of time, I expect that Garland was subject to some kind of punishment, or Sealing, afterwhich, he is not heard from for a considerable time.
-Interlude-
The world changes dramtically, due to either continnetal drift, or the effects of the Paradox.
-Final Fatasy 3-
???BC:The Archsage Noah(most likely descndant of Lukahn)masters all magic and tames the King of Dragons Bahamut and the serpent Leviathan.
When he dies, he splits his powers three ways-magic to Doga, Dreams to Unei, and his mortality to Xande, who feels cheated. Desch and Owen create the floating continent to protect the wind and fire crystals.

This still has a lot to be added, please wait for updates.

I believe in parallel universes in FF worlds, (well not really belive but you get the point) Al those universes are connected just as in Kingdom Hearts (duhuh)