This is what I had in mind as a thought organizer for example. This one's not free, however.
http://pc-shareware.com/images/scrn-snipits1.gif
Journal/diary software might be more date-focused, rather than allow you to just write thoughts in topics and categories. That's why I'm thinking maybe some outlining or organizer software would work better for you.
http://www.tgslabs.com/pictures/winorg/main.png
But this looks free, and useful with some categories.
http://www.free-downloads.net/programs/Advanced_Diary