If you'll recall, I mentioned how there were multiple paths in the Zelda series which made ordering the games rather complicated. Well I've finally got the Hyrule Historia, and can give a better description. There are actually 3 branching time lines in the Zelda series, All 3 of these time lines are alternate realities which means it is impossible to categorize all the Zelda games in one order because they are following different orders of events. The time line splits after the events of Ocarina of Time, so the first order of the games are as follows.

Legend of the Goddess and the Hero Time Line: After the events of Skyward Sword, Demise uses his power to create a never ending cycle of reincarnations so he can spend eternity claiming his revenge on Zelda and Link by having them constantly reborn. It is speculated Ganondorf may, in fact, be Demise's reincarnation. The games in this series include

Skyward Sword, Minish Cap, Four Swords, Ocarina of Time

The Decline of Hyrule and the Last Hero Time Line: Ganon successfully defeats Link and Zelda during the final battle of OoT. He obtains the Triforce and turns the Sacred Realm into the Dark World. The Sages imprison Ganon in the Sacred Realm as a last resort, but a new Link is born many generations later when Ganon is about to be freed. The series includes

A Link to the Past, Oracle of Ages and Seasons, Link's Awakening, The Legend of Zelda, The Adventure of Link.

The Twilight Realm and the Legacy of the Hero: In this time line, the original Link successfully defeats Ganondorf in the final battle and the sacred realm remains protected. The games in this time line include

Majora's Mask, Twilight Princess, Four Swords Adventures.

The Hero of Winds and a New World: In this time line, Ganondorf is resurrected and Hyrule is sealed before it is flooded. The games in this series include

The Wind Waker, Phantom Hourglass, Spirit Tracks.