Here is my theory on the Zelda timeline (some of it is taken from Game Trailer's theory, but it's not exactly the same, as there was stuff in their theory I didn't agree with). The main important thing to remember throughout the whole thing, is that a lot of the time it's a different Zelda and a different Link in each game. The hero of Hyrule is always named Link after the original hero, and the princess is always named Zelda after her ancestors (all the Zelda's are from the same family line, but not the Links).
First, Minish Cap is the earliest adventure. I think most people agree with this.
Next, comes Ocarina of Time...where Ganondorf is first introduced and is seeking the Golden Power so he can take over Hyrule. It is in OoT where two seperate time lines in the Zelda universe are created. In Hyrule A...Link fights and defeats Ganondorf as an adult. Hyrule B, is created when adult Link is sent back by adult Zelda to his childhood...to the time right before he first met her. Young Link and Young Zelda then change history, by warning the King about Ganondorf before he has a chance to take over. So....
Hyrule A - Ganondorf takes over Hyrule, and is defeated by adult Link after he has been king for 7 years. Link is then sent back in time to his childhood, and completely disappears from Hyrule A.
Hyrule B - young Link and young Zelda warn the king about Ganondorf before he can take over.
Now, let's start with the Hyrule A timeline.
After Ganondorf's defeat, he is sealed away in the Golden Realm by the 7 sages of Hyrule (as seen in Ocarina of Time). Hundreds of years later, he is still sealed...but now is using the wizard Agahnim to help free him. So, A Link to the Past comes after Ocarina of Time in the Hyrule A timeline. Agahnim must capture the 7 decedents of the 7 sages who sealed Ganondorf away in order to break the seal. Of course, since A Link to the Past came out way before Ocarina, the 7 sages and their decendents are all humans now (or Hylians, like Link and Zelda) and not different races like Gorons, Zoras, etc, like they were in Ocarina of Time. It's a plot hole, but that's what happens sometimes in these kinds of cases. Anyway, the current Princess Zelda is a decendent of the Zelda in Ocarina, who was one of the sages...so Agahnim kidnaps her. A new Link is called by Zelda telepathically to rescue her and defeat the wizard. Of course, Link also ends up going into the Golden Realm (which has been changed into the Dark World by Ganon), to defeat him...who is now pig like in appearance due to the Golden Realm changing your outward appearance to match your heart.
After Link destroys Ganon, he sets sail away from Hyrule to seek out new adventures...which leads into Link's Awakening. The booklet clearly states that it takes place after Link destroys Ganon...and the fact that the Link's nightmare that he fights at the end of the game takes the shape of how both Agahnim and Ganon looked in A Link to the Past confirms that Link's Awakening comes next.
After Link's awakening, comes the original Legend of Zelda...which once again possibly takes place hundreds of years later. Ganon is resurrected by his minions, and he still holds the Tri-force of Power which he got in Ocarina of Time. The current Princess Zelda (who's descended from the other Princess Zeldas) still has the Triforce of Wisdom, which as been passed down to her. The whereabouts of the Triforce of Courage, which the Ocarina of Time Link had...are unknown. Ganon kidnaps Zelda to get her piece of the Triforce, but before he does...she splits it into 8 fragments and hides them. Then, a new hero is called into action by Zelda's handmaiden Impa...named after the original Impa from Ocarina. The new Link collects all 8 fragments of the Triforce of Wisdom, destroys Ganon, and saves Zelda.
This now leads into Zelda II: The Adventure of Link...which takes place just a few years later. A wizard puts Zelda into a deep sleep when she won't tell him the secrets of the Triforce, and Ganon's minions mean to resurrect him once again, by killing Link and sprinkling Link's blood on Ganon's ashes (hey, it's in the booklet). Link now sets out to find the missing third piece of the Triforce, the Triforce of Courage to restore peace to Hyrule and awaken Zelda.
The next game in line is either Oracle of the Seasons, or Oracle of Ages. I agree with Game Trailers' theory, that each one probably takes place in a different time line then the other...so it can be either one taking place here. I believe this is currently the last Zelda adventure in the Hyrule A time line.
Now, we go back to Hyrule B...this is the timeline that is created when Link (who was sent back from Hyrule A) and Zelda warn the king and stop Ganondorf before he can take over anything in Ocarina of Time.
Navi departs from Link, but he soon sets off to find her with his horse, Epona. This leads into Majora's Mask, where Link must save