I 2nd OneNote. I used it extensively in college. You can migrate in chapters of a pdf textbook, OCR the text, and then highlight and annotate to your hearts content. It supports hyperlinking, which I used to make an interlinked glossary that spanned textbooks. You can 'print' any document/webpage to onenote as well as take screencaps. I still use win+shift+s to clip portions of the screen.