An advantage to using CPAN for a Perl application distribution (as if it were a module) would be the way CPAN.org automatically enables a logged-in user to use the annotation feature for a module's POD, and the way it ties into CPAN RT bug tracking for the module.

And the Kobes CPAN search site provides other goodies: an easy link to the CPAN ratings system and the automatic creation of a discussion board at CPAN::Forum.