http://phpxref.sourceforge.net/
"PHPXref is a small Perl script that I hacked together to make working with the source code of a large PHP site somewhat easier.
To this end it does two things:
Cross references functions, variables and database tables defined and used across your various PHP files
Generates documentation for each function defined in the PHP files by utilizing formatted comments placed next to each function
The output is a tree of HTML files that can be downloaded and browsed on a local machine without having to setup a web server, etc. "