Network visualization is one of the central tools of modern biology. I like this style of zooming used in a graphic on human disease from Redefining Disease, Genes and All in the NY times. (Based on a paper called The Human Disease Network from the Barabasi lab).
Cytoscape Web is slick. Christian Lopes and Max Franz have managed to reimplement a good part of Cytoscape (a desktop Java/Swing program) using Flash, Flex and the Flare visualization framework from the Berkeley Visualization Lab.
The March 2010 Nature Methods has a nice supplement on visualizing biological data.