i am jumping back to pen and paper or more of direct hand interfaces . I also recently bought graphic tablet for storing handwritten notes.From what i think computer can help you store ideas vertically,with excel you can have vertically as well but still the interface is the keyboard and not whole hands. vague thoughts!!
You're touching on a reason I like paper too -- in a digital format, I end up thinking too much about how I'm going to organize the information as opposed to just getting my thoughts down.
Organizing the information is important too, but worrying about it before your thoughts are clarified is a quick way for me to get pulled away from my focus on the problem.
