vlogger [1] is a nice piece of software to deal with large number of virtual hosts. It is meant to work with apache by piping the logs to the vlogger process that will then take care of storing them in you log directory.

I found an excellent howto that describes how to install vlogger in debian [2] .

To better integrate it with webalizer you can use this small bash snippet to generate conf files automatically for all your vhosts. This assumes that your log files are stored in /var/log/apache2 and that you don't have any other directories there but those generated by vlogger.