Move SSH off port 22, block direct root access (require user to log in through a user account, then su to root).
Use a WAF (web application firewall) like mod_security.
Refer to
PHP Security Consortium (they have a great audit),
SANS: Computer Security Training, Network Security Research, InfoSec Resources (lots of resources)
Validate and sanitize all data on the server side, optionally on the client side.
Keep all applications and other software up to date, upgrade.
Avoid duplicate instances of code, so a single upgrade will resolve issues.
Monitor the server - including new files.
Block access to MySQL from external sources.
Be especially wary of contact email forms and any other opportunities where users can post data.
Check applications for security vulnerabilities at
http://secunia.com before installing them.