I'm really sorry this thread was derailed by people who wanted to complain about the question instead of providing an answer. I found the thread by searching for exactly what the original poster asked: what tools are helpful for laying out non-linear plots? Thus, I have to say the meaning of the question was perfectly clear to me.
I've looked at Storyspace and it has possibilities, but there's no documentation with the demo version and the buttons are far from intuitive. Instead of feeling like a natural tool, it spawns multiple versions of the window I'm trying to type in and performs other oddities. I think I've looked at every tool made for writers and none of them do what I want to do -- keep track of plots that fork frequently or flow from multiple hubs -- without either overkilling me with writing theory or forcing me into something too rigid to permit recursion.
