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Define a "good website". What will work for you depends on lots of variables. I preper a "getting started" book at the very top of the TOC because some of my users are not familiar at all with the product. We also have a "What's New" section for those who are but just need to know what's changed since the last version. Next a "Getting Help" section of how users can contact the company and use the help file. Then I break the books down into the different modules we sell as part of our software. Each book is then broken down into the sub-sections relevant to each module. This works for us but may not work for you. Think about what you'd like if you were a user and go from there.
First, a web site generally requires an entirely different "layout" than help documentation.
Most web sites are mainly "reference," "marketing," or "sales" material, and will usually run from 20-50 pages.
As Colum has already explained, most help docs can run 2K-4K pages, and will consist of everything from version information (plus release notes) to New Features to Contact Us to Features broken down by function (Installation, User Controls, System Administration, Configuration, etc.), This is usually the "layout" for your TOC.
In addition to the TOC based on this layout, we have evolved our doc to a more "webby" look by changing our home page to include multiple navigation links based on "User Roles" (by industry-specific user titles), "Functional Tasks," "Major Components," "Menu Help," and "Reference." Each of these links brings the user to a page with 20-50 other links, grouped logically.
We found that the major complaint was "I can't find anything!" Adding this additional structure has so far elicited positive feedback. We're also hoping that as users find topics related to their needs, they'll learn where those topics live in the TOC, so that they can find things more easily in subsequent trips.
A well-designed Index used to be helpful, but I think today's "Googleized" users can't do anything but "Search"! And until RH provides a better search engine in a future release, you need to provide as much navigation help in your "layout" and/or find another search engine to incorporate into your help.