One of my favourite hacks at the last.fm Hack Day last weekend was a visualisation of musical connections between people in the Hack Day group. I partly liked it because it visualised a specific collection of people rather than the whole network, but also partly because of the amazing visualisation, which was made using Skyrails.
Skyrails is a C++, OpenGL-based network visualisation tool that presents nodes and edges in 3D space that the viewer can fly through. The nodes are interactive, the expansion of nodes is suggestive, and it can load in data dynamically from a server.
The current project of Skyrails developer Yose Widjaja is with biologists at the University of New South Wales on visualisation of protein interaction networks; there's a gallery on Flickr.
It's Windows-only and not open source; I'm looking forward to getting it started without it crashing :-)