Yes, The Legend of Zelda series DOES have an order to it
The following quote comes from an interview between Eiji Aonuma and the Official Nintendo Magazine:
“Yes, there is a master timeline, but it’s confidential document! The only people to have access to that document are myself, Mr. Miyamoto and the director of the title. We can’t 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 can’t 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
Finally, we know the truth about all of this nonsense! Granted we’ll probably never know for sure exactly which games go where, but at least having the knowledge that we’re not all crazy is wonderful news!