Bryan L is wondering how people take notes in their books. I only write in books when I vehemently disagree with the author. As a former librarian, I considered it almost as bad a dogearing your page corners. Don’t do that. Please.
Anyway, on the few occasions that I do write, I only use pencil and I’ll write wherever there’s space in whatever direct and place. I also use post-its, which are much better because then I can move them to around my computer screen for when I’m blogging or writing a paper with reference to the book.