I was thinking about what I'd like in a PDF-only supplement, the kind that's never intended to be sold as a printed book. How could you take advantage of the electronic and user-printable nature of PDF?
Let's leave off the bookmarks, because those should always be there. The only time they might not is when the content is less than four pages. We also assume that end users can print material from the PDF.
First, every character write-up on a separate page so they can be printed and used directly, without having. That means that the design of the write-ups is useful at the table as well as pretty.
A reasonably-sized graphic of a character that doesn't give away the secret ID (if there is one), so you can show the players, "Hey, he looks like this."
In fact, if the same write up had space so that you could annotate it (and the PDF allowed it), that would be great.
Cross-links between write-ups and mentions of the character. If clicking on the character's name took you to the write-up, that would be nice.
Maps on the page would be nice: a way to print maps automagically, or to print only certain layers of maps so that the GM could plunk down the map before destruction and later after destruction.