Until the chalkboard gets here, I've been working with FreeMind, a mind-mapping free software for Pocket Full of Posies and plotting out the Zombie Dating Guide. I gotta say, for a free program, it ain't bad. :) It's very simple to use and I'm sure I haven't even plumbed the depths of this handy program.
I'm primarily using it for character mapping for PFoP, I'll have use another page for plot (though that may wait until the chalkboard, I like to e-x-p-a-n-d more than is allowed on a computer screen). For zombies, it works quite well for chapter headings with their dropdowns.
What do you use to organize your thoughts? Paper? Software?