Reading notes
I use reno to create reading notes.
From this marked PDF Document:

i get (after some edits) this org-mode snippet:

where i can
- change some quotes to headers
- edit exported text
- add some notes for me
Play with source code
I can mark some challenges:

and pack the source code in #+begin_src and #+end_src blocks to evaluate it with org-babel.

Later i can export the notes from Emacs to a Pdf file to read it later again:
