Because I knew there was no way my answer to this question would fit in comment (other than to say: I use Dramatica), I made a post. Then it was too big (I think it was all the code though) for one post, and then too big for two posts.
How I Plot My Longer Stories:
Plot Progression (http://stephaniejo84.livejournal.com/12502.html) Plot, Theme, Genre (http://stephaniejo84.livejournal.com/12225.html) Characters and Illustration (http://stephaniejo84.livejournal.com/11941.html) (If you later planned on asking about characters, or really any of the things I'm listing here—no worries, I didn't go into detail on any of them just on how I plot them.) Weaving (http://stephaniejo84.livejournal.com/11676.html) The End (http://stephaniejo84.livejournal.com/11392.html)
no subject
How I Plot My Longer Stories:
Plot Progression (http://stephaniejo84.livejournal.com/12502.html)
Plot, Theme, Genre (http://stephaniejo84.livejournal.com/12225.html)
Characters and Illustration (http://stephaniejo84.livejournal.com/11941.html) (If you later planned on asking about characters, or really any of the things I'm listing here—no worries, I didn't go into detail on any of them just on how I plot them.)
Weaving (http://stephaniejo84.livejournal.com/11676.html)
The End (http://stephaniejo84.livejournal.com/11392.html)