After Darwin: Seven Ways of Looking at a Protein
"From the molecular biologists' point of view, this is simply an example of necessity being the mother of invention: They needed to understand the structure of things they can't see. But considered as a way of seeing the world, protein visualization illustrates how a digital craft can find truth not in convergence on a single canonical representation, but in letting a thousand flowers bloom. "

If you're interested in data visualization, you have to check out the Mappa Mundi archives.

Here's one web app I'd like to see: maps of the world that would show data (natural resources, population, battles, and so on) as they evolved through time. Games such as Civilization, Alpha Centauri and Ages of Empires use primitive versions of what I'm talking about to show how a game unfolded.

04/02/01 update: Larkfarm has all these great map links.

06/08/01 update: Software for the 4th Dimension.

07/20/01 update: MapMachine by National Geographic.

11/02/03 update: Animated map of the evolution of the US.