Organize Your Prose Project with Writer’s Café

The Storylines module on Ubuntu Linux
I’ve recently started brainstorming for my Master’s thesis, and turns out I’m actually going to have to do some story writing and plot outlining for the project. Seeing as I know pretty much nothing about constructing a story or developing a plot, I started doing some research on software that might come in handy for such a project, and I found this: Writer’s Café.
From the website:
Writer’s Café is a set of power tools for all fiction writers, whether experienced or just starting out. The heart of Writer’s Café is StoryLines, a powerful but simple to use story development tool that dramatically accelerates the creation and structuring of your novel or screenplay.
I’ve actually been pretty impressed with the application. The Journal and Notebook modules are fairly simple, but the Scrapbook seems like it would really useful for any creative writing project, and I have to say I am very impressed with the Storylines component. The way it allows you to manipulate virtual notecards on multiple timelines is just plain cool, not mention really handy for organizing your non-linear thoughts into a more cohesive whole.
How do you organize your thoughts when it comes to writing long-form projects? Notecards, a personal wiki, mindmap? Let’s discuss at the forum.
