As any zelda fan who has several zelda games has noticed, it is confusing to try to figure out what order the games go in. NES zelda first? ocarina of time? minish cap? where does link's awakening happen? after ocarina? after majora's mask? before a link to the past?
Well, no one really know's these for sure, because unlike with metroid, Nintendo hasn't released an official timeline for zelda. It onlygets more confusing if you take you questions to the internet, as there are countless conflicking theories and ideas. some say they absoluty know for sure, without a doubt, EXACTLY what order the games come in, while still others honestly say that that can't be sure, because there is simply not enough data to possitively prove much of the timeline, much less all of it.
The truth is, no one knows for sure, but we can all have fun coming up with theories, and making timelines, finding holes in others timelines, and in the end, we all know more about the world of zelda and the events that occur in it.

To break it down, there are two main types of timeline theories. Those are the split timelines, and the liniar timelines. The difference between these two timelines is what happens to the timeline in ocarina of time. Split timeline theories say that when link pulled the master sword out of it's pedistel and was frozen in time for seven years, he created a split in the timeline, leaving two seperate worlds, with two seperate fates of hyrule.
One, known commenly as the "child timeline" takes place in the world where link returns to his childhood with newfound knowlage of Gannons evil plot, and alerts the king of his intentions. Thus, causing gannon to fail, and the destruction he reaps in hyrule not to take place.

Where as, on the other side of the timeline, often called the "adult timeline" link is unable to stop gannon, because he's trapped in time for seven years, and has to fight gannon personally, where the sages seal him in the spiritual realm, former resting -