I'm taking over as a system administrator on an existing LAMP server for a site with a number of individual applications. The person I'm replacing has done a pretty good job with security as far as I know, but I'd like to take any preventative measures I can.
With the OWSAP top ten web vulnerabilities as a good place to start, what are critical things to check? I'm looking for both high-level concepts as well as specific things to look for (e.g. file permissions, open ports).