Interesting software for mind-maping/brainstorming ideas called Scrapple. Currently free while in beta.
In short, then, Scapple is a tool for getting early ideas down as quickly as possible and making connections between them. The main advantage of doing this in Scapple instead of on paper is that you don't run out of paper (the Scapple canvas expands to fit as many notes as you want to create), you can move notes around to make room for new ideas and connections, it's easy to delete and edit notes, and it's easy to export your notes into other applications when you know what you want to do with them.
In the past I've used software like this to plan out large projects (i.e. a website with a whole bunch of content/pages) and I've found it really helps because you don't have to worry about connecting things together like in a spreadsheet or text document right away - just dump it all on the "page" and connect the dots afterwards.