This can be somewhat of a hot topic (believe it or not) between readers who like to write in their books and readers who like to leave them unmarked.
Mr. Adler, mentioned in a previous post, encourages us to interact with the book by underlining, making margin notes and writing your insights. This engages more senses to improve the learning process. Also, old and rare books are increased in value if people of the times wrote in the book--it becomes a piece of history. In other words, they are leaving their footprint on the book for others to follow.
On the other hand, if anybody has tried to read a used textbook with rampant and gratuitous highlighting, underlining that goes through the words and awkward phrases in the margin, you see not everybody who leaves a note in the book is as historically valuable as we would hope.
Of course, any of you taken to task by the teacher for writing in your middle school textbook will know there are others out there who are rabid preservationists. Those who leave the book in mint condition as long as possible. Some go so far as to alter their reading stance in order to contort around the book so the spine doesn't actually bend. Not everyone is that bad, though.
On the other hand of that, books can often be a fluid commodity. They pass like dollar bills from hand to hand and shelf to shelf. If every person felt compelled to note in the book, there would be no more room left for the text!
Who is right?
My answer: Nobody... or Everybody
It really is a personal preference. It can also be different for the different types of books you read. A fun fiction book might not need too much attention. An exegetical text might beg more interaction when you are analyzing a passage of scripture.
My personal preference is to sticky-note the book as much or as little as I want. That way, I can take notes and interact with the text but also take them out eventually if I want to hand the book on to someone else. I also figure that what I have to put down in the margin isn't so intellectually stimulating that someone 150 years from now would want to read it.
No matter what you decide, the idea is to immerse yourself in the book and enjoy the experience. However, this little video covers the how-to-mark-a-book style (with the option of sticky notes) in a very nice way.
*The Preservation Faux Pas video was featured on www.ala.com (the website for the American Library Association). The How to Annotate a Book I found from searching on YouTube.