Here are my answers to the question “How do you organize your notes?”
Notes? What notes? Just kidding. I have folders of organized files sorted, by series: people, places, types of starships, terms, technology, races, star charts, names of starships, stages of civilization, types of travel, travel times, time dilation, backstories, additional misc. notes, deleted scenes, weapons, and lots of other stuff. I’m a junkie for notes.
I don’t do notes on plot. I figure out what general story I want to tell, and who I want to experience it. I then write the first scene with that person, then figure out where I want to go along the way. It is a very organic process. I do a lot of writing in my head.
Please go to the blog and read all of the other excellent answers to this question – I Read Encyclopedias For Fun