(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.
While the exact output options aren't immediately visible, the Imgur site says that Graphviz was used, in the tree layout, and a force directed layout (probably sfdp).