I came across this program whilst looking for something other than word that was funtional as a campaign writing tool. They have a collapseable tree structure that's pretty handy.
Of course it costs money (natch).
Treepad link. Then some more googling and I found this one more geared towards GM's directly
Myinfo. Then I found one that operates like the shareware programs thats free.
Keynote, granted it doesnt have all the bells and whistles that the other two have (its free) with Treepad being the "fanciest" however Treepad is the only one I found that has a Linux version without running Wine.
Anyhoo, just thought I'd throw those out. Didn't know if they've been discussed before or not.