Squirrel,
A technique I use for taking notes is to first write a paragraph or two of my thoughts and summary of the book/article immediately after completing the book. Then, if time allows, I write up the answers to a list of questions similar to that which IRDreams provided above. I rarely spend more that 10-20 minutes writing the initial two paragraphs, but have found it extremely valuable for retention and later reference when writing papers and exams. Also, if I own and plan to keep the book, I will take notes in the margins so as not to loose thoughts I have while reading, a technique which also helps me retrace my thoughts once I am done with the book. These notes in the margins are rarely longer than 5 words.
Hope this helps and good luck!