If some docs need to be generated, then I was using phpDocumentor, although I have also tried APIGen as well (phpDocumentor 2 beta was a little buggy for me). phpDocumentor comes with a report that can highlight incorrect commenting .e.g. a missed `@param`, or no short description, or `@param` of the wrong type compared to what has been type hinted etc.
WP-Parser is what's going to be used for developer.wordpress.org, since that will also handle the new hook documentations as well, so it's worth keeping an eye on that too.