While going thru my old projects to see which would be of any use to the open-source community, i came along an old project of mine, WebFM (Web File Manager).
I was applying for my previous job when i was asked to write a filemanager demonstrate my php abilities, the time alloted for this undertaking was 2 days, and i'm sure they wanted something a lot simpler, so i may have gone a little over the top when writing this, but i did felt i had a point to make :-)
Its Written for PHP 4, but i'm sure with some minor modifications it can be made to work fine with PHP 5.x too.

To configure this file manager for all virtual hosts and hide the script from the virual host's document root
place fm.php in a dir outside of the document root.

For example /var/www/fm.php, and the images in /var/www/fmicons then configure Apache aliases in your httpd.conf to access them as such:
 Alias /filemanager '/var/www/fm.php'
 Alias /fmicons/ '/var/www/fmicons/'

then you can use the file manager on any virtual host thru http://localhost/filemanager

Ofcource you can also use this configuration on a per-host basis (inside the section)