When I read a book, lately I've been very diligent about going back and reviewing some of the key points on each chapter. After much reading, I found that sometimes it is hard to find passages I highlighted and might want to come back later. So I keep a running list of notes on the book itself.
Words I've never seen, new reading material, and comments on each chapter are the 3 main types of notes I take. Some of my books have sections highlighted, underlined, or starred and this helps a lot when revisiting the books. But you can only scribble so much on the margin. The lack of space in the margin and the tedious task of flipping through pages I've already read when I want to review something, pushed me to come up with a this very simple review-as-you-go method.
Whenever I start a new book now, I take a big block of post-it notes, the ones that are like 4x6. I then take one post-it and stick it on the inside cover, then one at the end of each chapter. The one behind the front cover serves me to write down words I don't know. The one after each chapter makes it easy to write a few notes to summarize what I've read. If needed, sometimes I add more pages as I go.
Don't get me wrong, I still write all over my books. Some people consider scribbling on books somewhat of an irreverent practice, but I don't care; it helps me retain more content when I read. I wouldn't for example write in a nice dictionary, encyclopedia or coffee table book. But all other types of books go.
Update: 2012 may. - I think it's amazing how easy it is to do this with the Kindle. Now the only question remains is whether you can export or save your notes and highlights as you go through the book in kindle format in order for you to blog about it or quote the book or use it in your essays. That should be an upcoming blogpost.