You can use Joomla!'s default modal (
digitarald.de/project/squeezebox/ ) and use a external link menu as a handler to open that modal.
Inside that modal you can publish and module you want (Since the markup and module position will be in your index.php page you can do pretty much everything).
Alternatively you can also use another lightbox engine (preferably one that uses jQuery) like Fancybox or Colorbox or if you are on Joomla! 3.x you can use the modal from the bootstrap framework.
twitter.github.io/bootstrap/javascript.html#modals