Gareth Heyes has pointed out an interesting tool today for analyzing the source of your application and trying to discover security-related issues: RIPS

RIPS is a tool written in PHP to find vulnerabilities in PHP applications using static code analysis. By tokenizing and parsing all source code files RIPS is able to transform PHP source code into a program model and to detect sensitive sinks (potentially vulnerable functions) that can be tainted by userinput (influenced by a malicious user) during the program flow. Besides the structured output of found vulnerabilities RIPS also offers an integrated code audit framework for further manual analysis.

The project site lists out the features that come with the tool, what it searches for (including command execution issues, header injection, file manipulation and SQL injection) and some example screenshots of its interface. You can download the latest version and try it out for yourself.