Take a look at this Farnham Street blog post. Fascinating. I have a system for taking notes in relation to my current book, but as for general reading, I no longer read hardcopy books, so marginalia becomes a different concept. I do use Evernote, I do note highlights in ebooks as I read, but I’ve no systematic sensible repository for such digital marginalia. Thinking about it now, I shall have to come up with something. It makes sense.