Hackers or script kiddies often end up defacing and hijacking your website. They can do this because you are not looking! Or not loking hard enough.
An antimalware/antivirus scan for linux would be a good thing as it would allow you to scan files on your server on a periodic basis(using cronjobs). Mostly backdoors are uploaded [...]

Opcode caching helps!
From the eaccelerator home
eAccelerator is a free open-source PHP accelerator, optimizer, and dynamic content cache. It increases the performance of PHP scripts by caching them in their compiled state, so that the overhead of compiling is almost completely eliminated. It also optimizes scripts to speed up their execution. eAccelerator typically reduces server load [...]