OpenBSD mcl package created by Andreas Kähäri. (I am not sure if the given URL is the best available link, but openBSD people surely know their way around).
BioLayout is a powerful 3D graph visualization and analysis Java application, allowing interaction with large graphs in 3-dimensional layouts. It can handle graphs with up to and over 70,000 nodes, has many modes of operations and supports many graph queries and analysis modes. BioLayout has a facility to cluster the graph using mcl (the implementation available from this page). The resulting cluster structure is interpreted as a native class attribute and displayed by assigning colours to (the nodes in) clusters.