I've talked about Jeffrey Heer's, prefuse toolkit. Written in Java, prefuse supports various interesting information visualization techniques and is particularly good at animation. For example, Heer and danah boyd conspired to implement visualization and navigation of Friendster.
Heer, Card, and Landay have a paper in CHI 2005 that describes the toolkit from a research perspective. Meanwhile, Heer's MS report digs into the internals of prefuse a bit more. Interestingly the toolkit is actually fairly simple in design concepts and should be easily portable to other GUI toolkits. For example, building a prefuse like toolkit in Python+wxWindows should be straightforward, given the paper and the prefuse source code. This would be worthwhile to get a hold of some benefits of Python relative to Java.