Refactor, Encapsulate Fields (Generate getters and setters):
gode-generation-t5140.html?highlight=refactor

PHPDoc Analysis:
It analyzes your source code (whole project or single file) and find for missing/incorrect class/method/attribute doc comments. If it finds any problems, you will have the option to auto-fix the problems such as adding @param field if its missing, or remove unknown @param fields.

Additional, it would be nice if we can add doxy comments by right clicking a class/function name.

actually, you can implement most (if not all) of this functionality using php, then integrate it into PhpED, like it's done in these cases:
http://forum.nusphere.com/integration-scripts-results-window-preview-confirm-t4926.html
http://forum.nusphere.com/php-manual-function-search-t4970.html
http://forum.nusphere.com/php-code-coverage-t3802.html