My primary project at the Southern California Earthquake Center is called OpenSHA, an open source framework for seismic hazard calculations. OpenSHA is a Java-based platform. Originally we used simple executable Jar files for our standalone applications, but we have recently migrated to using Java Web Start.
The benefits of Java Web Start include automatic download of updates, native desktop integration (Start Menu/Desktop shortcuts/Mac OS X dock).
We have two parallel releases, a stable release and nightly builds. The nightlies automatically built with Cruise Control. As many of our applications use both Apache Tomcat and Java RMI, we run parallel RMI registries and Tomcat contexts, one which is linked to the trunk of our repository, and one which uses the release branch for the current stable release. This allows for easy development of server based applications, without disrupting the stable releases.
The website is build with Drupal, a content management system.
Check out the new OpenSHA website here: http://www.opensha.org and try out an application!