These programs aren't strictly Mindstorms related, but they may be of interest to Linux/Lego fans.
LeoCAD is (as the name implies) a CAD program for constructing and renderging Lego models. There is a usable GTK port, which can be found at http://leocad.gerf.org/linux.htm. The author implies that it doesn't have full functionality, so this might make a fun project for someone.
Sets of Lego pieces have been created for use with the popular POVRAY 3-D rendering program. You can find the pieces at http://www.kawo1.rwth-aachen.de/~witte/projekte/lego/lego.html and POVRAY at http://www.povray.org.