Alright, from this info, this is my timeline...
The Minish Cap
Vaati unleashes evil into Hyrule.
The first Link seals him away with the Four Sword.
The Zelda in this game is eventually cursed by a wizard into a deep sleep.
Four Swords
Vaati is released from the Four Sword and kidnaps the second Zelda.
The second Link uses the Four Sword to seal him away again.
Ocarina of Time
Ganondorf takes the Triforce of Power and takes over Hyrule.
The third Link and Zelda are given the Triforces of Courage and Wisdom.
Now this is where it splits:
OoT: Adult Ending
Ganon is sealed away in the Sacred Realm.
Link is sent back to the past.
Wind Waker
Ganondorf escapes from the Sacred Realm and attacks Hyrule.
The goddesses flood Hyrule turning it into the Great Sea.
Ganondorf sends the Helmaroc King to find the next Zelda
Years later, the fourth Link's sister is kidnapped by the Helmaroc King.
He finds the Master Sword, restores its power, and kills Ganondorf, sealing Hyrule under the sea again.
Phantom Hourglass
Not sure of the story in this one.
Now, the Child Ending
OoT: Child Ending
The third Link sets out to find Navi with Epona.
Ganondorf is sent to the Twilight Realm by the Sages
Majora's Mask
The third Link chases the Skull Kid to Termina.
He saves Termina from Majora's Mask.
He returns to Hyrule.
Twilight Princess
Ganondorf contacts Zant and gives him the power to take over the Twilight Realm as king.
The fourth Link is sucked into the Twilight Realm and meets Midna.
Together they defeat Zant and kill Ganondorf.
Unknown
Fifth Link finds Triforce.
Oracle of Ages/Seasons
The fifth Link is transported by the Triforce to Labrynna/Holodrum.
He saves Nayru/Din from Veran/Onox.
Twinrova tries to bring back Ganon, but only creates a mindless imitation.
Link defeats it and leaves Hyrule for parts unknown.
Unknown
Ganondorf is resurrected.
Four Swords Adventures
Ganondorf releases Vaati from the Four Sword to create a diversion, while he steals the Trident of Power and becomes Ganon.
The sixth Link defeats both Vaati and Ganon, sealing him in the Sacred Realm.
A Link to the Past
Ganon transforms the Sacred Realm into the Dark World.
The seventh Link defeats Agahnim at Hyrule Castle and saves the seventh Zelda.
Link defeats Ganon in the Dark World.
Link's Awakening
The seventh Link leaves Hyrule and washes up on Koholint Island.
He awakens the Wind Fish and escapes his dream.
The Legend of Zelda
Ganon is resurrected and kidnaps the eighth Zelda.
Impa finds the eighth Link to seek out the Triforce of Wisdom and defeat Ganon.
The eighth Link kills Ganon once and for all.
The Adventure of Link
The eighth Link gains the Triforce of Courage when he turns sixteen.
Impa tells him of the first Princess Zelda, and sends him on a quest to wake her up.
Ganon's minions try to kill him to resurrect Ganon.
Link defeats Dark Link and awakens the first Zelda.
