I'd still love to see a graphviz equivalent for JS that does layout for digraphs. This looks cool if you need undirected graphs, but doesn't seem to have any digraph support.
The tree layout supports some fairly complicated tree structures, including ones that alternate or have different configurations for leaves: http://www.gojs.net/latest/samples/tLayout.html
Disclosure: I'm a developer of this library and it is not free.
Here's an overview of the options for the layered digraph layout: http://www.gojs.net/latest/samples/ldLayout.html
The tree layout supports some fairly complicated tree structures, including ones that alternate or have different configurations for leaves: http://www.gojs.net/latest/samples/tLayout.html
Disclosure: I'm a developer of this library and it is not free.