While I was using a friend's PDFs at a game session, I thought it might be an interesting idea to have hyperlinks function between PDFs. The ones that are within the document are supremely useful (and as a GM that didn't have my corebook on hand, it made finding rule references rather quick to look up) but I think clicking on "Hardness" in the bestiary and it taking you to the Hardness rule section in the Corebook would be incredibly helpful.
I'm not entirely certain that there is a way to do this without compromising the security of the files, or if there's a quick-and-easy way for me to do it myself. I just thought I'd throw the idea by the folks here as a suggestion.