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 , 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?