Have you looked at Walrus?

http://www.caida.org/tools/visualization/walrus/

and then there is Nick Hemsley's Class Hierarchy Viewer project for
Croquet (Jasmine):

https://lists.duke.edu/sympa/arc/croquet-dev/2006-02/msg00004.html
http://www.squeaksource.com/CodeVis

Craig Latta wrote:
>     Does anyone have software that can draw a nice 3D visualization of
>large directed graphs? I wrote out a graph of a recent Spoon memory with
>object addresses as the nodes, in DOT (GraphViz) format[1]. There are
>many cycles, of course. :)  I tried Tulip, but can't get it to do much.