I could see Freemind coming in handy when it comes to character trees and such. Hey, I might actually do that. Great idea!
Scrivener looks interesing though, I'm not sure it's really suited for games and might be a bit "heavy". I guess, I'll use it for my next movie
I guess ideally, I would have a huge wall full of post-it notes but I travel a lot, so not so practical.
Today, I have experimented a bit with this Hypertext editor(Twine) and my impression is that it looks pretty usable and even a good way to prototype the game.