[faymontage]

(author here) The graphs are stock graphviz output, the linear layout is called "dot" (the default), and the nebulous layout is "sfdp". For your googling pleasure it's a "force directed graph layout", and there are many libraries to assist with it. d3.js has a force layout built in, for instance.

[tunesmith]

As far as I know, d3.js has force-directed but not "directed" force-directed like Sugiyama.