I recently uninstalled gnumeric, but the menu entry didn't go away. Looking through various menu items, settings, configuration options, etc., didn't yield anything. The online documentation for xfce 4.6 has the helpful statement that there is no documentation, and refers us to the xfce 4.2 documentation. I noticed in the same place that there was a link to 4.4 documentation, but no dice--that also refers us to the 4.2 docs. Clearly documentation has been a continuing issue in xfce. The 4.2 documentation led me to a page of misinformation (maybe it was accurate in 4.2), http://www.xfce.org/documentation/4.2/manuals/xfdesktop. This page shows an image of an "Edit Desktop Menu" button in the desktop settings window. There is no such button in 4.6.
A little googling led me to a lot of people asking how to do it, some suggestions that didn't work, etc. This reminded me of trying to get OpenOffice to stop "helpfully" suggesting word completions and spreadsheet cell contents: many complaints about how stupid the default settings were, many complaints about how difficult it was to disable, but solutions were few and far between.
Finally, fed up with trying to figure out how to do it the right away, I removed /usr/share/applications/gnumeric.desktop (actually I moved it to a safe place just in case) and, voila, the gnumeric menu item was gone.