Don't get carried away with it though...
Think of directories as projects; this project goes here and this other goes there...
Yesterday I was working on a site for a client. There were 8 pages to the project. She asked me to put each page in it's own directory so she can give out the urls without an extension... you know,
www.something.com/somethingelse
Since her site is not the only one I work on ( I have one client with over 60 websites), I won't remember the directory structure for the project files, and all of the related files have the same name: index.html (because they are all in their own directory)
These 8 webpages also used a total of 3 CGI scripts.
The next time I go to work on this site I will have forgotten what has been done, and each time I go to work on this project she can expect an extra 30 minutes added to her cost just because it will take me that long to re-learn the structure of this particular project.
I'm all about organization... just don't go overboard. This message hasn't even touched on the issue of portability.
Regards,
Steve MacLellan