I personally think:

MC> FS> OoT (child)> MM> TP> FSA> ALttP> OoA/OoS> LA
MC> FS> OoT (adult)> WW> PH

I dunno where to put the old Zelda games... Perhaps after PH... *Shrugs*

Wait, you actually took that seriously?

I like to think about it like this. Zelda has many ages.

Age 1: Zelda Fables: These stories occur before OoT when the Hero of Time came in.

Minish Cap - precursor to the Master Sword with the Picori Sword
Four Sword/Four Sword Adventure - Evolve the Vaati Plot
Oracle Games

Age 2: Hero of Time Stories.
Starts with OoT and the Timeline Splits.
The Child story goes like this:
After coming back thru time and realizing that his battle against Gannondorf will be intense, Link decides to travel to sharpen his stuff. Hence many adventures. First he travels to Termina (MM), and then gets shiped wrecked (LA), then he awakens a sleeping beauty that was placed under a curse (LoZ2:AoL). Then, when Ganondorf finally makes his move to over take Hyrule, Link fairly easily dispatches him (LoZ) and replaces the Master Sword to it's resting place. But that's when things go wrong. He defeats the current male of the Gerudo, but a nemesis from a previous adventure, Aganhim seemingly allies with the King of Hyrule. However, Aganhim truly wants to break the seal of the Dark/Golden Land and release a former male of the Gerudo, the one that made it to the triforce and had Vaati's trident (Alttp). Link defeats him and seals him back into the darkness.

The Adult Story goes like this:
It ends with OoT. Link is sent back and Ganondorf is sealed until the next age.

Age 3: Return and Final(hopefully) Defeat of Ganon:
Child: Ganondorf (older) corrupts the leader of the inhabitants to the Dark/Twilight world. The seals is broken and the descendent of the Hero of Time is called to duty (TP).
Adult: Ganondorf (younger) breaks out of his seal in an age when hyrule has completely changed. A new Hero of Time is awakened (WW and PH).

I know, it's a stretch, but I like it.

This is just when all the games were released, they are talking about the order of events in the series.

The best Zelda timeline explanation is that there is none. It is a series about a legend, and like all legends there are many versions of the same basic story. Games that don't explicitly draw connections to one another should not be considered part of the same version.

I think it would be neat if the last game in the series (assuming there ever IS a last game in the series) established itself as the true history behind the legend: what really happened.