Point site2pdf to a domain you want and it will save all of its pages to a single PDF:
ruby site2pdf http://12factor.net
This detects all "internal links" (links to pages on the same domain), crawls these and joins them together. The target for my development process was 12factor.net which is well written checklist and guide for your development and deployment.
There are a couple of dependencies: you need rubygems and wkhtmltopdf (compiled with qt in order to get all URI:s into the same PDF document).
Download site2pdf on github: https://github.com/chelmertz/site2pdf (code is subject for a lot of refactoring when I'm completely out of other stuff to do).