I think the order of the Zelda games is...

This is the order I think the zelda games are supposed to come in:
(Just so you don't get confused, there are five different Links)

1)Ocarina of Time (of course) (Link #1)
Here it splits into two time lines because ocarina of time has two endings: one
as a boy and the other as an adult.
2).a)Majora's Mask (Link #1)
Starts off in the OoT ending as a boy.
b)A Link to the Past (Link #2)
Roots from the OoT ending as an adult. This is a new Link. I don't think he's
a descendant of the original. Ganon breaks the seven sages seal.

(The rest root off from A Link to the Past)

3)The Legend of Zelda (Link #3)
4)Adventure of Link (Link #3) The names of the towns are that of the seven
sages so it must have rooted from the adult Link ending in OoT.
5)Oracle Series (Link #4) Link leaves Hyrule.
6)Link's Awakening (Link #4) Link starts off in a ship, just how the Oracle
Series ended. Link is lost at sea in the end so he never returns to Hyrule.
7)The Wind Waker (Link #5) Explains the story of OoT, part of ALttP, and the
disappearance of Link. Hyrule vanishes and a new land is created.

I still don't know where Four Swords, Four Swords Adventures, and the Minish Cap fit but that's just because I haven't played them.