OK, here is my 2 cents again.
1. PHP SU_EXEC
2. Ruby scripting support
3. Full support for ClamAV instead of Dr.Web or atleast an option to use ClamAV and so it will show up as protecting the client's email address as currently it still show AV off if not using Dr.Web.
4. A module for mod_security which allows for custom editing of the rules.
5. When upgrading via the updater, the email which is generated should have a clear list of config files which were overwritten and the name of the previous config file which can be rolled back if needed. IE: php.ini, httpd.conf, proftpd.conf, smtp_psa, ect..
6. SMTP threshold limits: Ability to set overall server thresholds for sending emails. IE: Client can send up to 1000 Emails but any attempt to send more then that will be trapped/ported to a database and the admin notified. You could have this ability on the Client or domain level and have a new Max emails sent limit.