The xfce4 ebuild is placing xfce specific programs (e.g. Xfdiff) in the Gnome "Applications" menu. This is most likely because of the new freedesktop.org specifications which places all .desktop files in /usr/share/applications. I tried adding OnlyShowIn=XFCE to the .desktop files but this didn't work. Others on the Gentoo Forums have reported the same problem. Reproducible: Always Steps to Reproduce: 1. emerge gnome 2. emerge xfce 3. log into gnome 4. click "Applications" Actual Results: XFCE specific applications (such as Xfdiff, or XFCE file manager) are in the Gnome "Applications" menu. This is undesirable, as a Gnome user is unlikely to want to run these, and would rather run the Gnome equivalents. Expected Results: XFCE specific applications should only be seen in the XFCE menu, not in the Gnome "Applications" menu.
The standard specifies one unified directory, which is $datadir/applications/
This has been discussed upstream and the behavior may be changed a little with upcoming releases, but otherwise its assumed to be the correct behavior