Your server is like your baby, and no one wants to see their baby crash, get kidnapped, freeze up, get attacked, or contract a deadly virus. One way you can lessen the possibility of security compromises on your server is to provide your web hosting clients with script installation services.
A lot of security holes come from user-installed scripts that are incorrectly installed or are not updated with the latest developer-distributed security patches. Joomla, for example, may generally be pretty secure, but older versions may have serious security flaws that newer versions have fixed. It is left up to the user to constantly keep their web software updated.
Script installers, which are usually integrated into web-based control panels, allow the users to easily run automated installations of popular web applications. Once installed, the control panel will also keep track of updates and allow the user to easily install the latest versions. The scripts are installed to your specifications to ensure the tightest security. It will automatically set permissions, delete install folders, and make it easier for the user to keep track of installed software and remove unused scripts.
Although many users may install a variety of scripts, you can generally bet on a few common free and/or open source applications that most users will install. This will not completely eliminate security holes, but it will give you far fewer to worry about from your clients. You can contact your control panel vendor to find out if there is a script installation plugin for your panel. If not, you may be able to find a stand-alone one that works just as well.