Hi there. I have been reading the boards for about a week now before I actually decided to register an account, and I have found many arguments as to what takes place where in the timeline of the Legend of Zelda. Being a Zelda fanatic myself, I have tried to figure out the chronological order behind the events that take place in Hyrule for some time. I have spent many a night searching on Google, Yahoo!, etc.; and I now present to you the information I have found thus far, in deep analytical detail. Please note that this post will more than likely contain spoliers for every game - however, only those spoilers relating to the Wind Waker will be highlighted, as it is the Zelda you most likely have not finished. Spoilers relating to the Wind Waker will be highlighted as such: This paragraph contains SPOILERS!, so you may skip over any information you may not want to see. You have been warned.
Link I
Our chronological journey begins with Ocarina of Time. You may argue that everyone knows it's the first game in chronological order, but I'm setting out to prove everything I post here, so let's look at why we can be so sure that it is the first. The instruction manuals for this game and A Link to the Past tell us that three goddesses descend from above and create the world of Hyrule from the chaos that they found. When their work was complete, they returned to their home, and the Triforce was left at the point they departed from. This became the Golden Land. We learn, during the course of the game, that as each race of Hyrule grew and evolved, they each came to desire the Triforce. Their greed caused them to begin the Great War, which came to a conclusion when the King of Hyrule began peace negotiations with the other races. During the Great War, Link's mother is badly injured and dies upon entering Kokiri Forest - the Great Deku Tree takes pity on her and allows her son to grow up as a Kokiri. Thus, the events of Ocarina of Time occur - this is the Imprisoning War that we read about in the instruction manual for A Link to the Past, where the gate to the Golden Land is accidentally opened, and Ganondorf Dragmire acquires the Triforce.
This paragraph contains SPOILERS!
Of course, there are many problems with the logic that causes us to come to this conclusion. You might argue that the stories of Hyrule's creation are different in the OoT and LttP manuals, but they are essentially the same, the one in LttP's manual is merely more detailed, providing information we learn in OoT while playing the game. Also, the LttP manual states that the Master Sword was forged to resist the Triforce's magical power, and states that Ganon was the reasoning behind this action, however this error can be summed up as a lack of historical accuracy on the part of the Hylians, as the LttP manual states that the Book of Mudora is a collection of legends and lore, or basically the Hylians history book, so several centuries had passed before the history of the Imprisoning War was actually written, and details were no doubt lost through generations. This also explains why the 7 sages are referred to as "Wise Men", and why the Hylians think it was a gang of thieves (led by Ganondorf) that opened the gate to the Golden Land. No doubt that Hylian historians would never be so bold as to blame the rise of Ganon on their beloved Hero of Time (assuming his legend carried on to the LttP time period). As for Link returning to his childhood in the end of OoT, this does not create 2 realities in Zelda - as we see when we get to Hyrule Castle in Wind Waker, Ganon can still control his army while he is imprisoned, and it is only when the King of Hyrule casts a spell on the Master Sword that Ganon's evil magic cannot continue to harass the Hylians. This explains the different looks between the castles in OoT and WW, as the OoT Hyrule Castle was still destroyed by Ganon's minions in the 7 years when Link actually aged normally. The reason the Hero of Time didn't defend the people when Ganon returned (thus the need for the flood, and the spell on the Master Sword), was because so much time had passed at that point that he was likely already dead of old age.
This paragraph contains SPOILERS!
Next we have Majora's Mask, this is a side quest young Link embarks upon after being sent back to age normally. Contrary to popular belief that the Hero of Time lost the Triforce of Courage when he was returned to being a child, I believe that it was when he first enters Termina that this occurs. This is because Ganon is sealed away even when Link returns to being a child, which leads me to believe that so long as a Triforce bearer doesn't leave Hyrule or the Golden Land/Dark World, the Triforce is his/hers permanently, and can be passed down through the generations (which explains why Tetra has a piece of the Triforce of Wisdom). When Link left Hyrule and entered Termina, the Triforce of Courage broke into 8 pieces, which were scattered across the land. Since it was part of a relic of the goddesses, the pieces washed up in the Great Sea for the Hero of Winds to find.
Link II
This paragraph contains SPOILERS!
OK, now we have the Wind Waker, I won't go into that much detail on it. In the opening sequence, we learn that Ganon arose again after his defeat in OoT, but the Hero of Time didn't not appear to stop him (most likely because he was dead). The goddess flood the land of Hyrule, and voila - we have the Great Sea. Even more time passes (so this game is must be more than a century apart from adult Link's time). During this time, the custom of dressing like the Hero of Time when you reach the age at which he set off on his quest to save the world (I remember reading somewhere that the exact age is 12, I don't remember where). About half way through the game, we learn that Hyrule still exists beneath the ocean, and by removing the Master Sword we free Ganon from the restraints on his power. In the end, we learn that Ganon began with noble intentions, wanting the Gerudo to have peaceful, happy lives, so he sought the Triforce. He was corrupted by it's power, as that was the strongest desire in his heart. In the end, Link plunges the Master Sword into Ganon, an act which we would assume actually kills Ganon (this information becomes vital when I introduce the next games), and the Master Sword is left at the bottom of the sea, thus Hyrule is washed away forever. However, we assume it returns when the Master Sword is eventually retrieved (and it must be, as we acquire it in LttP). Link III Next are Oracle of Seasons and Oracle of Ages, occuring one after another (which game comes first is a matter of opinion and doesn't effect the overall chronology in any major way). The reason this occurs after WW is that when you play both games one after another, the final boss is Ganon, who is brought back to life through the sacrifice of Onox and Veran. Wind Waker is the only game where Ganon appears to actually die (at this point in the timeline, I'll reveal later in my analysis why I don't think these games occur after LoZ or AoL).
Link IV
This paragraph contains SPOILERS!
Now we come to A Link to the Past. The manual itself states that the game takes place many centuries after the Imprisoning War, and since it has been established that the events of OoT are those same events described by the account of the Imprisioning War in the LttP manual, this game occurs now. After defeating Ganon in LttP, Link sets out for new adventure, to hone his skills as a warrior. This is when Link's Awakening occurs. My research has brought to my attention that the official Nintendo guide for LA itself actually states that LA takes place shortly after LttP. Link V Finally, we have the Legend of Zelda, and then Adventure of Link. The reasoning for this order is that I have found that the AoL manual states that it is the same Link from LoZ, and he has aged (to around 16 or 17, I don't remember). In LoZ, so I have read, Link acquires the Triforce of Wisdom (during the course of the game) and the Triforce of Power (when he kills Ganon at the end of the game). I have also read that in AoL, Link acquires the Triforce of Courage. This is basis of my arguement that OoS and OoA take place sometime between WW and LttP, since Ganon apparently dies in WW, but is in almost every game after it in the timeline. Also, you would think that since Link (in AoL) has all three pieces of the Triforce, that therefore he is all-powerful, and could be immortal (as the Triforce can grant any wish). It would be interesting to see what might happen after AoL, but that would require that the Triforce leave Link, and he is best qualified to protect it. This is unlikely, however, as i removes the solid ending point of the timeline where evil is no longer a threat and Hyrule can prosper under the watchful eye of Link.
Well, that wraps up my chronology of The Legend of Zelda series. I hope you enjoyed it, and found it insightful. However accurate I may be, remember that this is just a series of games, don't let the backstory ruin your enjoyment of one of the best video game series ever made. I'd just like to add that my generational numbering of the various Links is based solely on how each one looks, and is only based in information when the series actually provides us with that information. Thanks for reading, I'm off to play some more Wind Waker.