Scot McKnight has a helpful post on how to mark a book when you read it.
See also Mortimer Adler's more detailed essay on How to Mark a Book, which begins in this way: "You know you have to read 'between the lines' to get the most out of anything. I want to persuade you to do something equally important in the course of your reading. I want to persuade you to write between the lines. Unless you do, you are not likely to do the most efficient kind of reading."
