Hmm. I`ve never used the GUI. I`m always editing the files directly. But this new menu you are talking about... Is it a totally new right-click menu, or do you just want to add a new menu, inside the existing menu? Anyway, you should be able to add any items you want in the new menu, and remove them from the menus they were in.
Just did a new install of CrunchBang-11-20120927-amd64. The GUI menu editor doesn't appear to be working properly. I can add new menu items and edit the ones that I add. I can't change pre-existing items (the ones that were there from the install). The Execute line is empty for the pre-existing items. I can enter a program name, but nothing gets saved to the menu.xml file.
So, with 13.04 came Files (Nautilus 3.6). I think the UI part is fine, collapsing all the menu items to the single cog doesn't bother me too much, except in one facet. The HUD now no longer has access to those menu items.