After writing two articles on this subject (see Hyrule's Geography and Hyrule's Geography, Revisited), many people, myself included, were still confused about Hyrule's geography. Now, eight months after my last article on the subject, I am going to try with this article to eradicate much of the confusion going around. If you think that the maps in each game are totally inconsistent with each other, or if you want to brush up on your Hyrulian geography knowledge, this article is perfect for you.
Before you read this article, it is important to understand that none of the Hyrule maps, in-game or in-manual, are exact. They only give rough approximations of where everything is really located. Additionally, the in-game maps in older games are warped. This is due to the fact that Nintendo had to select a non-rectangular portion of Hyrule and squeeze it into a rectangular shape. This inevitably leads to warping and squeezing out of important details. Another important thing to remember is that the in-game map boundaries, such as cliffs, clouds, and trees, are not necessarily representations of real things. For example, the entire ALttP map is enclosed by cliffs, not because there are really cliffs there, but because the mapmaker didn't know what was there. The cliffs are just a placeholder covering up the real thing. Remember also that clouds are used as cover, so when you see clouds on a map that means it's hiding something.
The sections of this article are not presented in any particular order. You can skip around to your heart's fancy. I do have recommendations on how you read this article, though. It would probably be good to read What is Hyrule? first, to establish what exactly I and the games mean by the word "Hyrule." You might then want to read Landmarks of Hyrule to familiarize yourself with all the geographical features of Hyrule, which will be referred to throughout the rest of this article. You may then feel it necessary to see some maps of Hyrule drawn out. As I have long promised, I have hand-drawn maps available for your visual delight in Complete Hand-Drawn Maps. Last of all, if you're confused about how the OoT map works, and/or you want to know more about the mysterious "Death Mountain Area" in AoL, read The OoT Map and The AoL Map. If you need to look at a map from any game, there are links to them at the bottom of each page, below the Table of Contents.