wowzers .. heh
well i sorta do what bdl does ..
in my site directory, .. i have an 'include','images','classes' ( if i'm making the site OOP )..
it doesn't seem like one would really need more than that if you are using server-side scripting.
most large sites run off databases in which case the same scripts serves for hundres, or even thousands of pages.
you could make it appear like the end user is looking at a different directory for some content . sorta like how the tutorials section here on codenewbie is:
http://codenewbie.com/tutorials.php
but i use mod-rewrite to make it appear like tutorials is it's own subdirectory and each tutorial is its own html page.
http://codenewbie.com/tutorials/categories/
it make it appear more organized, but i do not really need that subdirectory for the content.