There are plenty of security schemes and strategies you can implement if you're a Shared Web Hosting company sysadmin however probably the most vital one is to install on Apache + PHP Webserver SuPHP module.
# apt-cache show suphp-common|grep -i descrip -A 4
Description: Common files for mod suphp Suphp consists of an Apache module (mod_suphp for either Apache 1.3.x or Apache 2.x) and a setuid root binary (suphp) that is called by the Apache module to change the uid of the process executing the PHP interpreter to the owner of the php script.
So what SuPHP actuall does is to run separate CPanel / Kloxo etc. Users with separate username and groupid permissions coinciding with the user present in /etc/passwd , /etc/shadow files existing users, thus in case if someone hacks some of the many customer sites he would be able to only write files and directories under the user with which the security breach occured.
On servers where SuPHP is not installed, all systemusers are using the same UserID / GuID to run PHP executable scripts under separate domains Virtualhost which are coinciding with Apache (on Debian / Ubuntu uid, gid – www-data) or on (CentOS / RHEL / Fedora etc. – user apache) so once one site is defaced exploited by a worm all or most server websites might end up infected with a Web Virus / Worm which will be trying to exploit even more sites of a type running silently in the background. This is very common scenarios as currently there are donezs of PHP / CSS / Javasripts / XSS vulnerability exploited on VPS and Shared hosting servers due to failure of a customer to update his own CMS scripts / Website (Joomla, Wordpress, Drupal etc.) and the lack of resource to regularly monitor all customer activities / websites.
Therefore installing SuPHP Apache module is essential one to install on new serverslarge hosting providers as it saves the admin a lot of headache from spreading malware across all hosted servers sites ..
Some VPS admins that are security freaks tend to also install SuPHP module together with many chrooted Apache / LiteSpeed / Nginx webservers each of which running in a separate Jailed environment.
Of course using SuPHP besides giving a improved security layer to the webserver has its downsides such as increased load for the server and making Apache PHP scripts being interpretted a little bit slower than with plain Apache + PHP but performance difference while running a site on top of SuPHP is often not so drastic so you can live it up ..
Installing SuPHP on a Debian / Ubuntu servers is a piece of cake, just run the as root superuser, usual:
# apt-get install libapache2-mod-suphp
Once installed only thing to make is to turn off default installed Apache PHP module (without SuPHP compiled support and restart Apache webserver):
# a2dismod php5 …
# /etc/init.d/apache2 restart
To test the SuPHP is properly working on the Apache Webserver go into some of many hosted server websites DocumentRoot
And create new file called test_suphp.php with below content:
# vim test_suphp.php
Then open in browser http://whatever-website/test_suphp.php assuming that system(); function is not disabled for security reasons in php.ini you should get an User ID, GroupID bigger than reserved system IDs on GNU / Linux e.g. ID > UID / GID 99
Its also a good idea to take a look into SuPHP configuration file /etc/suphp/suphp.conf and tailor options according to your liking
If different hosted client users home directories are into /home directory, set in suphp.conf
;Path all scripts have to be in
Also usually it is a good idea to set