The timeline of The Legend of Zelda has for some been a huge battle, many people had different ideas about what game followed which and if some games were even considered cannon. Gametrailers.com has recently released a new video that details the official zelda timeline, I've watched it and I must say its a very interesting video that goes into great detail on the history of the Zelda franchise. For those that just want a quick summarisation, there is not one, not two, but three different Timelines in the Zelda franchise. The three timelines come out of Ocarina of Time.
Its a really good video and one of GT's best, I recommend it completely.