We are using CAST to analyze our sources and prepare impact analysis when we receive change requests from users.
Take a look at their web site : http://www.castsoftware.com/
Their product is available for many programming languages and databases. YES, it's not a 3D interface, but if you want to quickly get a graph of an application or of a web site... well I think it's an extremely good tool.
A map of their technology coverage: