I've been happy with a paper notebook divided into three sections--Waiting, NAs and Projects. Each of those three sections is marked with those indestructible post-it flags. Someday/Maybe items are at the very end of the notebook, and as it grows it moves toward the front of the notebook. Allowing yourself to go back-to-front between sections will let you get the most use out of the notebook before you need another one. Each NA context gets its own page. There's a bit of flipping during my weekly (ok, monthly) reviews, but in the main it's very workable.

I don't happen to keep any reference info in this (although some of my project scribbles serve that sort of purpose), but a moleskine pocket or one of those multi-subject notebooks with pockets would allow for some reference storage if you were working on something that needed it. I think you probably want to make sure reference material can be kept without having to re-copy it every time.