When you right-click on the desktop in nautilus (or at least, in the version supplied by debian/testing at present, 2.8.2-2) you are presented with a context-menu containing, amongst other things, Create Folder, Create Launcher, Open Terminal, etc. It's the first and last entries here that cause a problem as they are right next to each other. I frequently right-click to spawn a terminal and accidentally create an empty folder on my desktop.
A new seperator
Adding a divider between the two entries turned out to be a one line job. However I think the Terminal entry is dropped altogether in CVS.