The most common way that sites and servers are hacked are through outdated scripts. No matter how much security you have on your server, outdated scripts create an exploitable hole. The importance of keeping scripts up to date is widely overlooked.
The 2 most commonly exploited outdated scripts are WordPress and Joomla sites.
Here's a simple way to find the version of all WordPress and Joomla installations on your server.
To search for WordPress installations, type:
find /home*/*/public_html/ -type f -iwholename "*/wp-includes/version.php" -exec grep -H "\$wp_version =" {} \;
To search for Joomla installations, type:
find /home*/*/public_html/ -type f -iwholename "*/libraries/joomla/version.php" -exec grep -H -e "\$RELEASE" -e "\$DEV_LEVEL" {} \;
Please note that this is a basic automated search and it may not find all installations. Even beyond the version of the main software, it is just as important to make sure all of the plugins, modules and themes inside them are up to date too, as well as all other types of scripts on the server.