Using the tree model for a Web site, each "leaf" represents a document, and a branch represents a link to that document. The main index then forms the root of the tree, and offers a route to each document. It is not guaranteed that this index will be the only way to reach a document! A reader can always bookmark a file, or locate it with a search engine and then go there directly. Make sure that each document can be used out of context.
To make it easier to follow the tree model, let the directory structure for the documents reflect it. Create directories for each distinc topic, even when there are only one or two documents concerning it. In the future, there might be more information on that topic, and then having the structure in place saves a lot of trouble. Trying to get the rest of the Web to change a reference is a nightmare.
Dividing the contents of your site into logical groups depends on who the expected audience is. For novices, providing a firm structure, perhaps also a "Guided tour", greatly helps to navigate the information. An experienced user might want to skip the introductions and go to the interesting material immediately. This reader has his own expectations about the organization of the information. If the site uses a different structure than they expect, they can become confused and be put off if there is no way to bypass it.
When making a reference, it can be useful to indicate what type of information can be found there. This allows a reader to determine if he should read the linked document. For example, "A step-by-step introduction is in the tutorial" or "The technical details are available in the reference section".
All documents should be available through more than one means. An organized index helps those who want to browse the site, but an alphabetical table of contents, or an alternative index sorted on some different criteria is very helpful. When the information is very technical, or there are many documents available, a local search engine is a useful addition.