Mine is taking stream of conscious notes with citations. Them taking these notes after finishing the work and creating an organized two page summary. This helps me when I need to go back to the work, if I can’t get enough from my summary, I have my notes, if they aren’t enough then I really didn’t take good enough notes.
Keeping a log has been really helpful for me too! What do you mean hypertext important concepts? You mean link to individual note pages?