Interesting article, thanks for posting. To mesh with the recent "Rands in Repose" post, this gave me some good relevance points to ponder for a little while.

I've developed a similar fascination with graph data over the past couple of years. My particular affliction has focused on treating program code as data (nodes) and stitched together with edges.

For visualization I was considering generating partial 3D models using something like StructureSynth and putting them in a 3D world like opencobalt. Also stumbled across Orange (http://www.ailab.si/orange/) which looks useful too.