Hmm, would putting labels work? That could include the chapter number, section number, and keywords. I usually go with topic and include the page number.

This is a great question though. What features could one add to a hypothetical PDF viewer that could help us? Sometimes I feel like having a separate text file is not sufficient, or not convenient enough. Most of the books I read do have a summary per section, perhaps I could take a screenshot of them. Additionally I could use the PDF viewer to highlight sentences, and add a feature to this PDF viewer that would allow me to cycle through them. Thoughts and/or ideas?