I Have Been looking at the Zelda "timeline" and I have figured out how Skyward Sword is canon and DOES come before the rest of the games. And if you go with the theory that there is a timeline, The goddesses create the world, they in trust The god
dess Hylia with the Tri Force who chooses The Demon King Demise as her hero. Wanting the world to be his own he gathered monsters and made his attack, creating a fissure in the world and murdering the people to try to get his hands on the tri force. The goddess took s chunk of the land and raised it into the heavens with the remaining people to get them away from the evil that plagued the surface. In order to keep it from falling into the hands of Demise, Hylia also sent the Triforce to The Sky and hid the portals to three pieces of the Triforce within Sky Keep, and enshrined the Goddess Sword inside the Statue of the Goddess, to be found by her next chosen hero when the time was right. This war took place thousands of years before the events of Skyward Sword. I have not played SKyward sword yet but I assume that Link rids the land of Demise and his monsters and the kingdom of Hyrule is formed shortly after. After that I set out to prove how Twilight Princess comes after Majora's mask, My friend insists that it can't because everything is different. According to multiple sources Twilight princess is set many decades after OoT. You play as a descendant of the OoT Link. Just like how in wind waker you are a Descendant of the hero of time, and a descendant of Zelda helps you. I know a lot of people would rather not have a timeline, but this is Official from Miyamoto himself. The Only glaring confliction I see is that the Minish Cap is supposed to come after Skyward Sword, however The ,Minish Cap is what spawns the Iconic green hat, why does Skyward Sword Link have the green hat? This has all been spawned by me watching this video..

http://www.gametrailers.com/full-episodes/en597n/timeline-the-legend-of-zelda

Also How does four swords come after TP?