I don't know if this will help you, but this is what I do...
Set your .htaccess file so directory index is your main file... ex: index.php
Then do your links like the following:
href="?content=page1"
then when you include $content, use:
include($content.".html");
to make it look cleaner, I wouldn't use content as the variable, I often use s or p. So you end up with really clean URL's, such as...
yoursite.com/?p=home
yoursite.com/?p=about
yoursite.com/?p=page1
It looks a lot better in my opinon, but I'm not sure if thats what you were asking.