3D rendering is done with povray.
A single frame 3d graph can be generated like this:
cat test.dot | ./springgraph.pl -p > test.pov;
povray +i test.pov +o test.tga -geometry 640x480

I did manage to create an mpeg of the animated frames with imagemagick ("convert -adjoin *.tga movie.mpeg" - you'll probably need to install mpeg2encode first.), but the mpeg compression did horrible things to the image quality.

If you generate one of these 3D graphs, you will probably want to modify the location of the camera so that the entire graph fits in the image nicely. The camera section is at the bottom of the .pov file. You'll want to edit the third (Z coordinate) value of the location.

VRML output

The above screenshot is, indeed, a vrml scene rendered by springgraph (with the "-v" flag), from phillylinux_full.wrl, which was generated from the same .dot file as the first two graphs on this page. Unfortunately, I've come across a lot of problems with vrml, and the latest seems to be lack of support for Text nodes, hence the lack of node labels in this file. The only vrml browser I've had any amount of success with is lookat. If you know of a vrml browser that works well under Linux, please let me know, so I can continue development on this feature. You may be able to use one of the other labeled graphs as a map when flying through this scene, but it looks like vrml aligns its axes a bit differently.