The directory structure should be logical and reflect the layout of your web site. It should delineate the logical framework of the web site, avoiding unnecessary cluttering of files in one directory. It should also help in segregating similar files.
For example, you should place all images on your web site in a separate directory, which you can name as images. Some web developers might divide this directory into subdirectories such as icons (that contains images used as icons or buttons) and backgrounds (containing images used as backgrounds on web pages).
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For this web site (www.webdevelopersnotes.com), I have placed files and web page belonging to each section in a separate directory. Images that are common for all web pages (like the logo and some bullets) are placed in the images directory and those that belong to only a particular section reside in its directory. Similarly, you can segregate PHP or ASP include files in an includes or appropriately named directory.
Naming a directory or a sub directory depends on you; just choose a logical directory layout. Tip: Actually, the file names and directory names do matter from a search engine optimization point of view.
Working on the directory structure for your site might be time consuming. However, it will help you in understanding the web site layout when you look at the site after 6 months.
