POD (Plain Old Documentation) is great for writing documentation inside your code. Perl comes with pod2html. pod2man and pod2text for processing it and there are a number of other translators available.

If you're interested in using Literate Programming with Perl, there's a good chapter on it in Andrew Johnson's book Elements of Programming with Perl

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<http://www.dave.org.uk>

European Perl Conference - Sept 22/24 2000
<http://www.yapc.org/Europe/>