[R] Graph layout software

[Sean Davis]

This is a bit off-topic, but I thought I would ask.  What are folks
typically using for graph layout when drawing graph structures.  I have used
Rgraphviz for relatively small graphs (100 nodes or fewer) with nice
results.  However, quick google searches turn up a number of graph layout
packages that look to be perhaps a bit faster and more flexible for larger
graphs.  Also, has anyone used graph layout software that works in three
dimensions?

Sean