flowboards and Cmap
I'm using flowboards for game design because they encourage a non linear approach. Good games branch.
I found out about flowboards and game play modes through an article by Ernest Adams at Gamasutra, Designer's Notebook: Designing with Gameplay Modes and Flowboards. To follow that link you need to sign up at Gamasutra, but it's free.
The graphic is not quite a flowboard. It's a flow chart that also shows game play modes, in red. Click on the graphic to see my larger version at my flickr account.
To turn it into a flowboard you would also need to show annotated pictures of at least the main game rooms: welcome, configure, gameplay and celebration.
I've made this in Cmap, which is free concept mapping software available from The Institute for Human and Machine Cognition (IHMC).