Thought I'd share this with the community. I've been using software called Celtx. It's free and has really helped me organize my project. While this software is really designed for writers of movies and plays, it works well with games.
In it, I'm able to document all of my characters, story-lines, dialog, describe levels, and music. I've included a sample screenshot.
I even took a game development template for creating an outline and dumped it in to help me get started. Can't remember where I got it, but it was a public freebie.
In Celtx you also have the ability to do storyboarding and some project planning. And the best part it that it's collaborative. You can keep your project stored on the web and other members of your development team can view/update your project if you give them permission.
You might want to check it out.
http://www.celtx.com/overview.html
"I'm trying to find new ways to make this game more attractive." - Dennis Rodman