On the HowTo Forge website, there's a recently posted article about using the IDS tool for PHP to help with intrusion detection for your website.

This tutorial explains how to set up IDS tool on a web server with Apache2 and PHP5. PHPIDS (PHP-Intrusion Detection System) is a simple to use, well structured, fast and state-of-the-art security layer for your PHP based web application. The IDS neither strips, sanitizes nor filters any malicious input, it simply recognizes when an attacker tries to break your site and reacts in exactly the way you want it to.

They show the steps you'll need to get things installed and working as well as some of the configuration changes you'll need to add/make (including the creation of an auto-prepend file to make using it all over easy).