Why is marking a book indispensable to reading it? First, it keeps you awake — not merely conscious, but wide awake. Second, reading, if it is active, is thinking, and thinking tends to express itself in words, spoken or written. The person who says he knows what he thinks but cannot express it usually does not know what he thinks. Third, writing your reactions down helps you to remember the thoughts of the author.
Over at The Millions, Dustin Illingworth explores the many merits of marginalia.