I have found a new favorite tool for brainstorming and organizing a module. Alright, I didn't so much FIND it as it was recommended to me by an PnP old-schooler. It is called FreeMind, and it is the right price for the title (free).
It is similar to MS Visio minus the myriad of icons and about 80% of the frustration. You can simply start with a root node and keep inserting child nodes as you work through things. Then, you can move nodes or trees of nodes into whatever hierarchy you desire. It also has some great export features such as HTML, XML, JPG, etc. Copying/Pasting is also a breeze to grab a list of nodes and pasting them into notepad or other text editor.
Anyhow, I think this is a great resource for any module developer who wants to throw their ideas down 'on paper' and then rearrange them. I know it has certainly helped me get the plotpoints of SoSIII:CoS worked out nicely. It always helps to have a visual reference and bonus if it is editable.
Sands of Solvheil Series
Design Document for Sands of Solvheil I: The Ruins of Kazatharis
Design Document for Sands of Solvheil II: Beneath the Hearleforne
Design Document for Sands of Solvheil III: Crusaders of Shalihir