Here’s Mortimer J. Adler’s suggestion for marking a book intelligently and fruitfully (from his essay, “How to Mark a Book”):
1. Underlining: of major points, of important or forceful statements.I have used all the seven methods to mark the books that I have read. But Adler notes that "marking up a book is not an act of mutilation but of love."
2. Vertical lines at the margin: to emphasize a statement already underlined.
3. Star, asterisk, or other doo-dad at the margin: to be used sparingly, to emphasize the ten or twenty most important statements in the book. (You may want to fold the bottom corner of each page on which you use such marks. It won't hurt the sturdy paper on which most modern books are printed, and you will be able to take the book off the shelf at any time and, by opening it at the folded-corner page, refresh your recollection of the book.)
4. Numbers in the margin: to indicate the sequence of points the author makes in developing a single argument.
5. Numbers of other pages in the margin: to indicate where else in the book the author made points relevant to the point marked; to tie up the ideas in a book, which, though they may be separated by many pages, belong together.
6. Circling of key words or phrases.
7. Writing in the margin, or at the top or bottom of the page, for the sake of: recording questions (and perhaps answers) which a passage raised in your mind; reducing a complicated discussion to a simple statement; recording the sequence of major points right through the books. I use the end-papers at the back of the book to make a personal index of the author's points in the order of their appearance.