There are many things to be wary of, one is the server itself with the vulnerabilities that might be hidden in it, but this requires a sys admin who knows his job and applies updates to the OS and the software.
The other side of the problem is script vulnerabilities, but I don't know of any php related article on the topic, there are however tons of articles for other languages. Search for "CGI secure code" or "PHP secure code" try also "coding" instead of "code" or "scripts".
Anyhow, I'm trying to gauge interest in such an article about writing secure scripts (or at least reducing security risks in scripts), let me know if you (and others) are interested in such a piece.