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Put "export DESKTOP_SESSION=gnome" in your ~/.ashrc and back it up and that variable will be set for all your apps, whether launched from the menu or terminal. Makes VLC look like gtk2 as well.
The the .desktop files in /usr/share/applications/ are from Debian, and I don't really want to start providing custom ones. But for packages that are basically broken in their menu items I will consider it. I will make one for minitube.