I use Dia. I don't entirely understand what you're trying to diagram, so I'm not sure how well it would work for you. I've used it for data flow diagrams, state transition diagrams and flow charts, and occasionally for entity relationship diagrams and UML diagrams (though it's not exactly good for those last two types). It's easy enough to use that I prefer it over paper. I don't think it has any way to automatically generate diagrams, though.
I've found most graphing software too clunky, or having too much mental friction, for my purpose of creating graphically represented plans, to convert written diagrams into digital form, or to do preference inference based on the structure of my goals (amongst other things).
So far the only tool that I've seen that reduces this friction is GraphViz [1], since I think I can literally just list down connection after connection in markup, with no care for structure or reasonableness, and then prune connections after I see how the entire thing looks. Point and click is for suckers.
However, I also like the approach of Freemind that quickly outputs a visual map that is easily traversable; but it doesn't do much for me when the causality is more involved.
Are there any alternatives that anyone is aware of?
[1] If you are not familiar with GraphViz, see this amusing introduction that maps the social network in R. Kelly's hit hip hopera, "Trapped in the Closet".