Now if you want to have an executable directory for cgi/perl scripts you need to make a directory in your document root for your scripts to be placed I always use cgi-bin
Here is what you need in your virtual hosts file for an executable directory
If you want to password protect files with .htaccess you need the following lines.
<Directory "/var/www/sites/yoursite"> Options Indexes Includes FollowSymLinks AllowOverride All Order allow,deny Allow from all </Directory>
This is always cool to have your own custom 404 error file you can also specify this in your virtual.