Note-taking Systems?

A reader named Russ sent me an e-mail asking about note-taking systems that I thought would be good to pose to the group:

Q. "Have you come across any useful system for marking a study bible? I want to avoid marking it with extraneous comments or in a random manner."

Here's how I answered: "I'm afraid I don't have a system and haven't really been convinced that they're necessary. These days, I tend to take notes not in my Bible but in a companion notebook, so I'm mainly underlining and bracketing passages in the text, and writing out whatever needs writing in the notebook. That way, if I switch Bibles (which I do pretty often in order to do reviews for the site) I have whatever I need with me. That's probably overkill for most people, though." But then I began to wonder. I was writing in my Bible with a ballpoint until my readers won me over to the Pigma Micron, so maybe this is another area where I need to be educated. Is there a good system for taking notes in a Bible? If so, I'd like to hear about it. I like how Russ described his goal -- "to avoid marking it with extraneous comments or in a random manner" -- because I can relate. Have I ever shared the story of my first Bible purchase? It wasn't motivated by a distaste for bonded leather or glued bindings. No, the thing that prompted me to make my first purchase (before which, all my Bibles had been given to me) was the fact that throughout adolescence, I'd been writing notes in my Bible which later proved rather embarrassing. In a college chapel service, I had my Bible open on my lap, and the person next to me started giggling. The more she tried to stop, the worse it got. I couldn't figure out what was so funny, but I started laughing myself, as you do. Afterward, I found out that she'd been reading the things I'd written in the margin of my Bible. (There were illustrations, too.) If I still had that Bible, I'd post a photo, but in my embarrassment I quickly replaced it -- and for a long time after that I was very circumspect in what I wrote! So if there's a good system out there, I want to hear about it.