The 1.4.x versions of phpDocumentor have the -ue option (--undocumentedelements) [1], which will cause undocumented elements to be listed as warnings on the errors.html page that it generates during its doc run.
Further, PHP_DocBlockGenerator [2] from PEAR looks like it can generate missing docblocks for you.
[1] -- http://manual.phpdoc.org/HTMLSmartyConverter/HandS/phpDocumentor/tutorial_phpDocumentor.howto.pkg.html#using.command-line.undocumentedelements
[2] -- http://pear.php.net/package/PHP_DocBlockGenerator