See our PHP Test Coverage tool from Semantic Designs:
http://www.semanticdesigns.com/Products/TestCoverage/PHPTestCoverage.html
Very low overhead, handles huge systems of files, intuitive GUI showing coverage on specific files, and generated report with coverage breakdown at method, class and package levels.
Best of all, no requirement to install anything in the system being
tested. No need for xdebug, etc., which means you don't have to argue
with the sysadmin to do your testing.
You can use it with PHPUnit to get unit-test driven coverage. Or you can use it on your website to collect coverage from any functional testing approach/tools you may have.