You can do whatever the hell you want with code copyrighted by you. If you do not own the copyright on all of the code you use (such as the inclusion of GPL'ed code within your own code), then you are subject to the lowest-common-denominator of licenses of the copyrighted works you are using.

Simply using other Perl modules doesn't count. You may be bundling them with your own code, but your product is not composed of a derivative of their code, you are simply re-distributing their code without modification. Even if you do modify their code, by distributing it you are simply releasing your modifications under their license (the GPL). This in no way "infects" your application.

Generally the code is yours to do with as you please, unless you have cut/pasted code written by somebody else into your own application, at which point (assuming it's GPL'ed), it's illegal for you to re-distribute the result without GPL'ing it in turn.