I have a scene that renders differently when rendering from the command line and using the GUI.
Specifically, objects go missing from the render when using the command line.
I use the following command (tested in OS-X terminal):
/Applications/blender-2.5x/blender.app/Contents/MacOS/blender -b GzContrejour.blend -o bl_out/render.png -F JPEG -x 1 -f 1