There is no substitute for pen and paper. Unfortunately, computers can crash. On the upside, when you type things out it always looks miles better than whatever that chicken scratch was you called your handwriting and it's a hell of a lot easier to read by candle/dim light. My current binder is a mishmosh of printed sheets in sheet protectors in a 3 ring sharing space with some quickly scribbled notes. When I feel that I've mostly completed this area of study, I'd like to have one of those BIG grimoires (the +$300 hand sewn binding kind!)
I'm a geek. I love nice fresh paper, and beautiful pens, and I hate breaking in journals of anysorts. But they're so prettyyyyy...