I keep a pen and small piece of paper with me as I read. I then write down anything that catches my eye, and reference the page number. I do this every time I read the book (every one I have read, I have read several times). When I am done, I leave that piece of paper in the book. Whenever I have a question about something, I can look over my notes to quickly find the answer. I also will review my notes on occasion to be sure I am doing everything I had intended to do when I read the book.
I will also mark pages I frequently visit with a Post-It note. I have found note-taking to be a very valuable time-saver. Writing stuff down also helps me to remember things I have read better.