I'll usually:

• Use a piece of paper as a bookmark on which I take notes (noting page numbers of bits I don't understand, attempts to summarize/reorganize, interesting insights, notes while I work something out, random ideas the text gives me) - it's not rare that I end a book with two or three pages of notes stuffed into them. I'll then go over those notes and maybe enter some bits in Anki
• Directly enter stuff in Anki if it's atomic enough (it often isn't)
• Takes notes in Google docs (either if I'm near a computer at a time, or if I want to have "searchable" notes or look up related info on the internet)