Structure really depends on the site contents. A docs folder is still pretty common (though many people name it PDF and then also put docs in it... haha) as is images. The biggest thing to look at is what the site has now and what it will have. For instance, if your site has a new comic every day, it might make sense to create a folder for each year with twelve folders inside for the months and name the comics by the day. The usual "about us," "contact us," "main page," etc. are often kept in the root directory, but it depends on how extensive the site is. Ultimately, you're trying to avoid clutter and stay organized with the future of the site in mind.
Check out Gordaen's Knowledge, the blog, and the MR2 page.