I've got a notion to develop to-do list software with an emphasis on dependencies for my own use; since I haven't written it yet I don't have any actual help for your question, but I'm curious what you mean by “preference inference based on the structure of [your] goals”, as it sounds potentially relevant.
preference inference based on the structure of [your] goals
It's nothing too formal - wisdom gleaned from an article here and a blog post there.
Most of us readily have a list of goals that come to mind, but it's likely that they are subgoals and we are unaware of why exactly we do them. So, you keep on asking "What will this goal do for me?" instead of "What will do this goal for me?", creating downwind nodes in your graph until you presumably hit your preferences. In which case you (a) could check your preferences for consistency and...
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".