The timeline of the Legend of Zelda, as requested by DM Malon

Here is a diagram of how the games go. The explanation will come after.

Line 1 (occuring in the Sacred Realm): A Link to the Past (starts right with OoT) > Windwaker > Link's Awakening > (Oracle of Seasons/Oracle of Ages) Phantom Hourglass > Spirit Tracks > Minish Cap > Four Swords > Four Swords Adventures > Legend of Zelda > Adventures of Link
Line 2 (occuring in the REAL Hyrule): Ocarina of Time (starts right with LttP) > Majora's Mask > Twilight Princess > Skyward Sword

Note: Oracle of Seasons and Oracle of Ages occur as a co-current parallel loop. No matter what, whatever you play first of these two is the first in their order, and the other is the second.

The explanation (prepare for HEADACHES):

Ok, the timeline works like this. In the beginning, Ganondorf (I will refer to him as Ganon) was sealed away by the seven wise men in the beginnings of A Link to the Past. However... they botched. The spell to seal him cast him into the real Hyrule, where he met his parallel other, the gerudo heir Ganondorf (this being the OoT Ganondorf). He told Ganondorf about the triforce and it's powers, tempting the gerudo king into trying to get the triforce. It was at this time that in Ocarina of Time, Zelda becomes suspicious of Ganondorf's actions and gets Link to find the sacred stones to stop Ganondorf's plans. However, by pulling out the Master Sword, OoT Link damages the seal the wise men placed, allowing Ganon's power to once more, reach the sacred realm. It is also at this time that OoT Link, Zelda and Ganondorf obtain their respective triforce pieces.

But wait a minute, if they have the triforce, how can it possibly exist in LttP?

The answer is simple. This is a parallel 'instance' of the Triforce, not the real triforce. This explains why the triforce is WEAKER in Ocarina of Time than it is in A Link to the Past. Regardless...

Because the seal is damaged, Ganon is able to get his power to corrupt the wizard (Begins with a A, but I can't spell it so bugger it). This gets LttP Link's events running to get the Master Sword.

But Dragoon, there is only one master sword (unless it's one of those parallel instance thingies) right?

Wrong. There are in fact TWO master swords. Both with very different purposes. If you noticed, the master sword in A Link to the Past has a GREY Hilt, not a blue one. You would think this is down to age fading it but look at Twilight Princess. Ocarina of Time's blue master sword still has a blue hilt. Also of note is the purposes of the two swords. The blue hilted sword acts as the seal to the sacred realm, as well as a seal to lock away evil. The grey master master sword is never referenced as a seal to anything, more as a sword to KILL evil (which indeed it does). Moving along.

When OoT Link goes to the forest temple, he encounters 'Phantom Ganondorf' and slays him, this breaks the seal fully, and sends Ganon BACK to his own world where LttP Link utterly pwns his face into the ground and kills him for good, while OoT Link goes on to seal away Ganondorf.

Wait wait wait, why does Phantom Ganondorf dying, send Ganon back to the sacred realm?

Because Phantom Ganondorf is GANON. The clue is his trident he is wielding. Ganon ALWAYS wields a trident (sacred realm side, this Trident was made to be the OPPOSITE of the Master Sword) while GANONDORF always wields a sword or punches people. The talk Ganondorf gives at the end of the forest temple is a bluff, to try and fool OoT Link.

Now for Windwaker, why is there a BLUE master sword in that game then?

Because as mentioned in Minish Cap, the master sword and it's chamber can traverse time and space to where it is required. Ganondorf in this game is the OoT Ganondorf, not the LttP Ganon (because he is DEAD). The simple fact is that the seal broke and by this time, Ganondorf wanted the REAL Triforce (because it was far more powerful than the one he had tried to get before). The Blue Master Sword traversed the boundaries between these two parallel worlds to where it was needed, but it was a extremely hard task even for the master sword, draining it of it's power. This explains why you gotta recharge it.

Now, the dark world and the twilight realm. They are parallel opposites just like the two Hyrules. The dark world turns the LttP Link into a bunny because that is what his soul reflected as... but why didn't he turn into a ghost, and why didn't everyone else?

Because parallels can have any number of differences. In this case, the dark world turned people into what their heart reflected. In the Twilight Realm, they became ghosts, more literal reflections of their souls. It was only because Link in Twilight Princess has the triforce of Courage that he turned into something else more reflecting the triforce's nature with him (which as we may or may not know, wolves are a good representation of courage as well as kindness, as they will even look after abandoned humans and let them become part of their pack, and are not afraid to challenge bigger animals like bears for food) It was by this very difference in parallels that explained why the master sword cured Link of being a wolf, and why LttP Link REQUIRED the moon pearl.

Is the Picori sword the Master Sword?

No. It is a entirely different weapon, made by the Picori in a similar manner to how the Magical sword was made, a sword made to repel evil. But it can't match up to the power to the triforce.