Deemer on Planning Your Story Architecture
I write hypertext using a powerful editor called Storyspace. If there's a better hypertext tool on the market, I don't know about it. Storyspace creates writing spaces, which you then can link together in various ways.
I'm going to structure my writing spaces in three columns. The central column will be the central narrative thread. The left column will be back story writing spaces. The right column will be miscellaneous writing spaces, including stream of consciousness, monologues, reviews and other newspaper items of the day, music files, and whatever else may be appropriate.