Above is my version of the Legend of Zelda timeline. Please note that no official timeline has been released by Nintendo, although they have promised one day that this will be revealed. Below I explain my version of the Zelda timeline. WARNING: Extremely long post.
Timeline Zero: 1st Hero: Gustav
This would be a game that would explain the coming of Hyrule. That is that Gustav Hyrule, a blonde-haired hero clad in green, no hat, with the Picori Sword in hand would bring about order to the war-torn land. Because of this, he becomes the first hero of the land that would bare his name. What little thus far is known about him was explained in the Minish Cap prologue.
1st Link
It would seem appropriate that this chapter would exist since the Link in Minish Cap was the first to don the trademark hat. While Gustav did the hair and outfit, the Minish Link was already named Link. This doesn't explain why all heroes that would follow would be named Link instead of Gustav. Like Zelda II that explains why all the princesses are named Zelda, there needs to be one that explains why all the heroes are named Link. This would most likely take place around the time of the Master Sword creation, perhaps the first hero to wield the legendary sword.
Minish Cap
The first hero since Gustav to wield the Picori blade, thus the reincarnation of the true hero. Unlike the 'hero of time' or the 'hero of the winds,' Gustav and subsequent reincarnations are simply the 'hero.'
Split Timeline Ocarina of Time
This broke the timeline in two. The first was created at the end in the dark devastated land of Hyrule that contained Adult Link. When Zelda sent him back in time to his youth Zelda remained in this world. Ganon was sealed away by the Sages and the people of Hyrule would rebuild. They would rebuild their homes, their villages, and the magnificant Hyrule Castle. The second was created with Link returning to his youth. He and Zelda would alert the king to Ganondorf's plan. This would cause Ganondorf to flee or face imprisonment by the king of Hyrule.
Timeline One: Wind Waker
About 100 years after Ganon was sealed away by the Sages in the Adult Link world, the land has since been flooded and is faced once again with Ganon's terror. The thing was that with Hyrule rebuilt, the citizens were enjoying a time of peace. Ganon broke the seal and returned to the land of Hyrlue, but when hero showed (no Link), Hyrule was defenseless. Ganon would soon have the Triforce until King Hyrule prayed to the Goddesses. They flooded the land and prevented Ganon from acquiring the Triforce. Fast forward to a new Link battling Ganon with a fully restored Master Sword. By driving the blade straight into Ganon's head, he turned to stone thus becoming the new Master Sword pedestal. Link and Tetra (Zelda) set sail to look for a new land of Hyrule, to look for 'their' land.
Phantom Hourglass
Shortly after Wind Waker, the 'hero of the winds' and Tetra came across the Ghost Ship which transported them to the realm of the Ocean King. Upon defeat of the great evil Bellum, the Ocean King took its true form. Appearing much like a tattoo-less elder Wind Fish, it transported Tetra and Link back to the realm of Hyrule. Having an argument with her pirate crew, it appeared much like Link's Awakening of 'did it happen' or 'was it just a dream?' New character Linebeck was actually from the realm of Hyrule since in the background at the end, you can see his ship sailing away from Tetra's pirate ship.
Timeline Two: Majora's Mask
Starting from the Young Link timeline, the youthful 'hero of time' began patrolling Hyrule. With Ganondorf on the run, Link would prevent him from returning. Enter mask-wearing Skull Kid. After an ordeal in Termina, with the clock resetting the 3-day period, Link spent a long time in Termina. While the clock reset to relive the same 3-day period here, Hyrule continually, moved forward in time. It is unknown if the 'hero of time' ever returned to the land of Hyrule.
Twilight Princess
Ganondorf on the run, cornered by the Sages out in the desert, they are able to subdue him. The Triforce of Power, which was thought that with time returning to before he touched that he wouldn't have it, but since he had it, then time returned prior, he still had it despite this. The Sages would imprison him in the Twilight realm. Ganon would taint the Twilight Realm and have it spread to Hyrule. A new Link would rise and stop Ganon with the Master Sword. Ganon would pull the sword from his stomach and flee again, although seemingly powerless without the Triforce of Power. Link would return the Master Sword to its pedestal in the Temple of Time, return to Ordon to see Ilia and inform her what he must do, then he sets off to bring about the end of Ganon.
TP Sequel
Picking up where TP left off, Link would pursue a fleeing Ganon, hopefully with the new Crossbow weapon in tow. Due to TP's darker theme, Link would probably only be able to stop Ganon and seal him away by sacrificing his own life, thus the first time that a Link 'died,' at least that was visible. Ganon would also ascend to the blue pig/Moblin form, dumping his 'human'-like form for good. Hopefully this would be released on the Wii, although if not would likely be released on the next Nintendo home console, the Wii's successor.
Legend of Zelda (NES)
Ganon returned with Power sought Zelda's Triforce of Wisdom. She shattered it, was captured and had her hand maiden Impa go in search of a new hero. A new Link with shield and sword in hand would rescue Impa then would take upon the challenge to defeat Ganon. He fought and killed Ganon.
Link's Awakening
After the destruction of Ganon, Link set sail to further explore. Against a mighty storm he crashed on Koholint Island which was actually within the realm of the Wind Fish. Link conquered the many challenges including facing his fear of the return of Ganon.
Zelda II: The Adventure of Link (NES)
Zelda and Impa decided that Link maybe the reincarnation of Gustav, so Impa told Link the true 'legend' of Zelda. Taking up this true test of courage, Link made his way to face his greatest fear, a fear that he didn't even know about, himself. Much like Luke Skywalker seeing himself as Darth Vader, Link came face to face with the reality of if he turned to evil. With the defeat of Dark Link, Link became infused with the Triforce of Courage and awakened the sleeping Zelda of old, thus proving that he was without a doubt the true reincarnation of Gustav. Ganon's minions would use this fight to secure some blood of Link, thus enabling them to resurrect Ganon.
Four Sword Adventures (GCN)
With the call to duty, Link pulled the Picori blade ( the Four Sword) from its pedestal. Defeating Vaati revealed the true puppet master as Ganon. Now with the powerful Trident weapon Ganon was far more challenging, but so was Link. With the Four Sword, Link wouldn't kill Ganon again, but he would seal him away.
A Link to the Past
A new Link would challenge the wizard Aghanim, who was actually a puppet of Ganon, whose seal had weakened. Link would travel to the Dark World and in the Temple of Power, face a Trident-wielding Ganon. With Silver Arrows, this Link would kill Ganon and then return the Master Sword to its pedestal in the Lost Woods. Was this the true end of Ganon? Only time will tell.
Non-canon Zelda CD-i Zeldas
Not much to say here but nightmare-inducing tragedies. So lets say no more.
Oracle of Ages/Seasons (GBC)
These two titles that would serve as each other's sequel were great homages to the Zelda franchise. With the Master Sword broken, Triforce leaving the land of Hyrule, and Twinrova seemingly alive and well (she died in Ocarina of Time), the Oracle games were great fan service, but not story canon.
Four Swords (GBA)
On the same game cartridge as A Link to the Past for its GBA rerelease, this served as the first multiplayer Zelda game. Four Swords Adventures (GCN) would replace it in the timeline and expand on the story.
Link's Crossbow Training (Wii)
Packaged with the Wii Zapper, this served as a shooting game demo. No story here, although hopefully the crossbow will return in the sequel to Twilight Princess.
~Strscrm2006
