Update
I now believe that the time line is:
Skyward Sword- this was announced as the prequel
Minish Cap- said to take place before OoT
Ocarina of Time- Split time after this game
Kid Time Line
Majora’s Mask- first game in kid time line
Four Swords/Adventures- "one of the oldest tales" and The game shows how Ganondorf gains his Trident and turn permanently into the pig beast, Ganon
Twilight Princess- 100 years after ganon/dorf failed to take hyrule + ganondorf has Pig ability
A Link to the Past- Link kills the unsealed Gannon and the Master Sword "sleeps forever"
Oracle of X/X- Link is transferred to Holodrum and then Labrynna and kills the half restricted Gannon and sails away to an unknown destination.
Link's Awakening- On the same boat Link sails away in at the end of OoX Link is seen on at the beginning of LA. One of the forms of the final boss is an altered form of Agahnim, this being a dream Link has to have already seen him.
The Legend of Zelda- not a direct sequel but follows LttP/OoX/LA
Zelda II: The Adventure of Link- direct sequel to LoZ, but both are following ocarina being link finds the triforce of courage for the first mentioned time
Adult Time Line
Wind Waker- centuries after the hero of time (Adult time line) and recollects the triforce of courage
Phantom Hourglass-direct sequel to WW
Spirit Tracks- takes place at least 100 years after WW and PH
Where Credit is Due
the following were contributed by
TwilightKing
ALttP- Link kills the unsealed Gannon and the Master Sword "sleeps forever"
OoX- Link is transferred to Holodrum and then Labrynna and kills the half restricted Gannon and sails away to an unknown destination.
LA- On the same boat Link sails away in at the end of OoX Link is seen on at the beginning of LA. One of the forms of the final boss is an altered form of Agahnim, this being a dream Link has to have already seen him.
and for the prequel revamp I thank
JuicieJ