These storylines tell the whole story of each individual game in as much detail as I could put in. They have much more detail than any brief, sweeping summary can provide. They try to tell a complete, accurate, satisfying story, following Link's adventure in a game from start to finish. They are a good read if you want to know a game's full storyline, and can be used as a good reference guide.
The storylines are not presented in any particular order. I have listed them in the order in which Nintendo published them, which is different from any possible internal order. The purpose of the storylines is not to suggest any particular continuity theory. They aim to give an impartial retelling of the storyline within each game, with as few theories thrown in as possible. As a supplement to the storylines, I recommend that you acquaint yourself with the different continuity theories going around. The most important of these theories are given in the Continuity section.
My storylines do, however, sometimes contain elements from other games, or narrative that tries to elaborate on a somewhat sparse or underdeveloped part of the game. I do this only to tie that particular game's storyline together, or to fill in gaps in the narrative. I believe that these additions are mostly harmless, and will only serve to augment the reader's enjoyment and understanding of the storylines. After all, the storylines would be of little value if they simply listed all the events taking place, without trying to connect them together or make rational sense of them. Newcomers to Zelda need to figure out what's going on in the story, and my storylines fulfill this need. More experienced fans should be able to tell which parts of the story come from that game, and which parts are strictly my own interpretation.
Note: The "Early Hyrule" storyline is not based on any game. It presents legends and accounts from all the games that pertain to the ancient history of Hyrule. These stories are, for the most part, consistent with each other, and are helpful in understanding the other storylines. It is suggested that you read this storyline before reading the others.
Without further ado, the storylines: