Java Web Start is a software distribution setup that provides a user with a HTML link to click on to automatically download the latest version of a Java application.
I'm not sure if this will work well for the Mars Simulation Project with it's size (~18Mb) and it's directory/file structure, but it's worth looking into.
Feel free to add more ideas to this page or add to its discussion.
02.12.2009: has been done for release 2.88