The Official Zelda Timeline
The Official Zelda Timeline is one of those that doesn't make a whole lot of sense. To start with it's pretty straight forward starting with Skyward Sword and following a direct timeline, but then Ocarina of Time, the N64 classic flips it on it's head to create two separate but equally plausible timelines: one for the Child Link and the other for the Adult Link. We are already presented with a problem in that both timelines cannot happen at once, then Nintendo revealed a third timeline to complicate matters even more!
In the Legend of Zelda: Ocarina of Time Link travels 7 years into the future turning from a child into an adult to defeat Ganondorf in the future. He is successful and armed with the knowledge of how to beat Ganondorf he travels back in time to defeat Ganondorf 7 years earlier as a child. This gives us the first timeline break, one where Link doesn't travel back into the past and one where he defeats Ganondorf at an earlier point in time. Both of these games cannot exist in the same universe, think of the paradox it would cause! If Link defeated Ganondorf in the future and then defeated the same Ganondorf in the past how could he actually defeat him in the future? Therefore Link cannot be in Majora's Mask and The Wind Waker if Majora's Mask follows the child Link and Wind Waker follows the adult Link.
The third timeline stems from whenever Link dies, this works for both adult and child Link. If either Link dies at any point Ganon is revived and thus ushers in the events of A Link To The Past and many other early titles including the original Legend of Zelda on the NES. These three timelines cannot exist all at once in the same universe, however, maybe quantum physics holds the explaination and link back to the theory I introduced when talking about the Slot Machine of what happened to Fox McCloud in Star Fox!
The Many Worlds Theory states that for every decision made a new universe is made for each scenario. In essence every choice you make creates at least two independent universes. Let's think about this in terms of the electron but more specifically the spin of an electron. At any given moment you look at an electron it could be spinning either up or down. Let's translate this to Russian Roulette and turn our humble electron into a weapon! If you're playing a game of Russian Roulette (do you play Russian Roulette? Not for long I guess) and you have a gun which functions off of this mechanic: if the electron spin is up the gun fires! Every time you pull the trigger the gun has a 50/50 chance of going off depending on the electron spin at that given moment. One universe is created where the electron is spinning down and you survive but pulling the trigger also creates the universe where the electron was spinning up and then, well, you probably wouldn't care that you created a new universe! Each round you go you are, in a way, jumping from universe to universe, in the end it won't be the same you that started the game (and that's not just because of the PTSD that would probably follow).
This then gives us a bit of an explaination to the Zelda Timeline. Each individual timeline is a separate universe, which itself can create even more universes and those universes can create universes! It also explains what happened to Fox McCloud, he flew through the Phoenix in his universe and wound up in a different universe ruled over by a giant Slot Machine! The faces on the planets tell you that you're not in the same universe anymore and perhaps he has ventured into the universe which follows child Link and Majora's Mask. It would also explain why the moon that hangs dangerously over Termina shares a lot of similarities with the planets that Fox sees in this new universe. But at the very least The Many Worlds Theory provides an explaination to an otherwise implausible timeline!