Using POD as the basis of documentation for Perl projects is the usual way to do. There are many modules available to convert POD into several formats. However, I was not able to find a module that creates a single PDF file from all the documentation available for e.g. a single project. Typically a series of PDF files are the result of a conversion. Combining these files and creating a hierarchical outline can be hard work.
As a simple aid, we peeked into pod2pdf and wrote a little wrapper around it in order to handle many files and create the outline. Well, this solution is not rock solid, as we rely on its internals but at least it is short and usually creating PDFs is not mission-critical.
Maybe some parts can still be improved, but for people interested, here is my first try: https://gist.github.com/2277444. Feedback welcome!