The Top 500 Supercomputers
list would be a good place to start looking for such projects.
Obviously most of the top supercomputers aren't dedicated to one particular purpose but usually themed around complex physics simulation projects.
You may be interested in the Japanese Earth Simulator
project which runs on the 4th most powerful supercomputer on the planet.
is good at explaining some of the kind of things they do with their mega processing power (currently ranked No.3 in the Top 500 list)
Interestingly the Earth Simulator is the only supercomputer in the top 10 that doesn't run Linux as it's core OS.