Just some minor addition to my previous post. A nice video showing a quick flight through such a 3D graph:

Please excuse the poor quality. There was quite something involved in producing this video:

1. Find a way to capture the render content. So the app now copies the OpenGL buffer to a
   Java2D buffer and writes it to disk using ImageIO (and that is done per frame with a fixed framerate).
2. Secondly finding a binary of ffmpeg or mencoder for MacOSX is not easy if you don’t know where to look (yep, I know: ask google).
3. As I wanted the video to look nice, I wrote some kind of director mechanism. So one can now automate actions within the 3D space using Groovy. Behind the scenes there is a fully timed command cue

All in all this is becoming really cool stuff