Coming from an Official Nintendo Magazine interview…

“Yes there is a master timeline but its confidential document! The only people to have access to that document are myself, Mr. Miyamoto and the director of the title. We cant share it with anyone else! I have already talked to Mr. Miyamoto about this so I am comfortable in releasing this information – this title [Skyward Sword] takes place before Ocarina of Time. if I said that a certain title was ‘the first Zelda game’, then that means that we cant ever make a title that takes place before that! So for us to add titles to the series, we have to have a way of putting the titles before or after each other.” – Eiji Aonuma

Wow! This is one secret I would love to get my hands on. We should hold a little competition to see who can come up with the best time-line.

Link