If a graph is simple, it's easy enough to just look through. For more complex graphs though, it's hard to make sense of if it's not arranged in a way that resembles how developers conceptualize a class or method hierarchy. Understandably, NDepend wouldn't be able to do this automatically.
Can I move graph nodes around by hand? Or alternatively, is there another program that I can export the graph to and rearrange the nodes there?
No so far NDepend' graph' nodes cannot be re-arranged and cannot be exported to another tool that lets achieve this. Did you try to tick or untick the cluster settings that will provoque re-arranging complex graph or sub-graph?
Same if you tinker with layout settings:
Also a screenshot of a graph that is not in a way that resembles how developers conceptualize a class or method hierarchy would be welcome.