Honestly. Pencil. Every single programming book I own, that I've actually read, is covered in hand written notes. I also tape post-it notes onto important pag

Honestly. Pencil. Every single programming book I own, that I've actually read, is covered in hand written notes. I also tape post-it notes onto important pages with more notes as bookmarks. It's free. Easy. Random access. Read/write friendly. "No sign-up required".