To my knowledge, Yed is the least worst existing graphing software.
I use it, as does Andrew Critch, and people at Leverage / Paradigm, generally.
Thanks to your advice, I've tried it for goal factoring and for drawing various diagrams. It's great! (by which I mean it's less awful than other software)
Is there software for goal factoring (the CFAR technique)? I want to use it to create a directed graph, which is not necessarily a tree and may have cycles (this requirement disqualifies mind mapping software). Nodes are goals, they have attached text. There's an edge from goal x to goal y iff fulfillment of x directly contributes to fulfillment of y. There should be an easy way to see the graph and modify it, preferrably in a visual way.