Last summer, I mentored Michael Landis as a Google Summer of Code student. He did a project developing a web visualization for phylogeographic and biographic analyses, looking at how phylogenies map to spatial locations. He did a really great job implementing things with modern web technology, using Polymaps to manipulate map tiles served from Cloudmade and using D3 to manipulate graphics SVGs. The Phylowood web application is hosted on GitHub and contains examples from influenza H5N1, rabies virus and the Vireya subgenus of rhododendrons. Hosting this on GitHub should make it easy for someone to fork the entire repo and swap in their own examples for easy sharing of results.
We just had the paper describing Phylowood published as an Application Note in Bioinformatics.