One of my biggest issues when working on story notes, especially world and plot building, is organization. The most difficult parts with regards to my personal creative process are:
I still lean heavily on analog notes given my computing devices aren't the best or the newest. If they die, I don't want to panic about losing so much precious work. There's also a tactile element to hand writing--the feel of the pen and paper, the texture of a notebook's cover, the scent of processed dead tree, the weight of a book in hand--that I find enjoyable and a boost to my creative mojo.
So, taking a lead from a friend, I've bought a nice, sturdy journal that I'm now transferring all of my finalized series notes for Gods and Monsters of Urth into. I'll still keep a separate "throw away" journal to scribble furious brainstorming in, but that could just as easily be a napkin or sticky note so long as the final info ends up in the big notebook!
Of course, owning cats (who are notoriously anti-written-communication and pro-paper), this might be an easier concept than actuality.
If you write, how do you keep organized? What works best with your creativity style? What methods have you tried that were utter disasters?