Some do allow this as an option to their launch command, some don't. Check the man page for the programs you want to do this for, to see if they support this. Another way around this - the one I use for Evolution - is to have Compiz open them on a workspace I don't use until I need them. To do this, go to ccsm>Place Windows>Fixed Window Placement>Windows With A Fixed Viewport and add your program.
Bookmarks