I think that dead paper is not the right medium for this. I love OneNote and how flexible it is. I can quickly open a note (faster then notepad on my machine) to jot down a todo or some snippet I need or I can open my project notebook and see all my "design meetings" (with myself) and it is searchable AND there is a way to encrypt sections. I've put my OneNote notebooks on dropbox and that's basically a perfect system for me.

The two things this is weak in are sharing and not having a leather bound tactile notebook and pen to play with which I must admit looks pretty cool.