http://phpxref.sourceforge.net/PHPXref is a great tool which builds an HTML-based outline of your source code. It's been an indespensible tool for working on a very large project, http://www.moodle.org/Moodle), especially when getting my hands dirty with a new section of code I haven't used yet as it makes following an execution path very easy to do.

From the site description:
        * Minimal requirements, minimal setup.
        * No web server required to view output.
        * Cross-references PHP classes, functions, variables, constants and require/include usage.
        * Extracts phpdoc style documentation from source files.
        * Javascript enhanced output provides:
                    o Mouse-over information for classes and functions in the source view.
                    o Hot-jump to the source of any class/function definition.
                    o Instant lookup of classes, functions, constants and tables by name.
                    o Search/lookup history.
        * Pretty-prints PHP files from the browser.
        * Stays crunchy in milk.