A friend had given me a question on being able to do some graph manipulation in 3-D, because the 2-D undirected graph was getting cluttered, I'm starting to explore ways to transform a 2-D graph into a 3-D one. Or really, because I'm lazy, instead I'll just end up working on wirting some software so you can do the 3-d manipulation yourself...
Of course, more likely, the forces of laziness and time will win.
Back to whence you came. More about this project may happen at some point in the unknown future.