The problem is that the project seems to be dead (last blog post in 2008) and is still in alpha. I am considering using it as my preferred visualization GUI, but the alpha tag scares me. Do you know of any alternatives to Ubigraph with similar functionality? Would you consider creating an alternative?
I ran into ubigraph as well, and was deeply fascinated by it. Unfortunately, its license said that you couldn't redistribute it.
Check out the FourDSocketProxy, which runs as a Node's library, opening a browser window.
Ubigraph does seem very pretty, but 3D visualizations suffer from occlusion problems that can significantly hamper their usefulness. It is usually better to have multiple 2D views side-by-side.
What size datasets are you interested in analyzing? There are several open-source tools for analyzing graph or network datasets that vary in the features available and the size they can handle. NodeXL is a great introductory tool that integrates network analysis into Excel 2007/2010 (Disclaimer: I'm an advisor for it). Other tools like Gephi, Cytoscape, and especially Large Graph Layout may scale better for larger graphs, but are not as easy to use. Pajek and UCINet are some proprietary alternatives.