Open Source Scientific Apps?

Paranoid Diatribe asks: "I'm a Unix admin for a scientific computing environment at a large public university. In the past few weeks, I've had the (dis)pleasure of dealing with several vendors to get their applications re-licensed to run on various machines. These are vendors of scientific applications like MOLGEN, apps from MSI, and S-PLUS. There are many others. The majority use the most evil of license managers, Flex-LM. I spend more time messing with Flex, license key files, and calling the damned vendors than I do actually administering the boxes they run on. As such, I am becoming very disenchanted with these commercial vendors. Is there a compilation of alternative scientific computing apps (GPL, BSD, or other open license would be preferable) and how they match up to their commercial counterparts? I'm aware of Freshmeat.net and a small list at the OpenGL site (though many of these are commercial as well), but I was wondering if there was a better list of such apps."