DoxyFilt* is Doxygen for Perl.
See also: Analyzing large Perl code base.
Update: If anyone has any questions about configuring their Doxyfile to run Doxygen/DoxyFilt under Cygwin, please /msg planetscape.
* Update: 2005-12-28 Kudos to both john_oshea and tfrayner for alerting me to the fact that my link above has been rendered usless by the foul creatures known as spammers... I have found what appears to be a good link to obtain DoxyFilt; the most recent version seems to be from August 24, 2005: Doxygen-0.84.tar.gz. Thanks again, guys!