[jcims]

Agree. Neo4j’s visualization tools are surprisingly painful to use. I’d love to find something that allowed you to trivially add code to the layout engine. Graphviz’s clustering capability seems to be unique among any of the tools I’ve used as well.

[specproc]

Gephi can cluster, but the algorithm isn't that transparent or flexible. I've increasingly found myself doing the clustering in Python and rendering in Gephi.