This is a known issue that has affected a number of users.
If you look on the bright side you now have a much cleaner menu, and you
can limit it to the few applications that you might want to run in dom0
(hint - very few.)
You can copy the files from out of a Fedora based qube if you have one.
If you still have the install medium then you can extract the desktop
files for applications that you want, by pulling them from the rpm
packages:
For example, to get the xterm .desktop file:
mount qubes.iso /mnt
rpm2cpio /mnt/Packages/x/xterm-318-2.fc23.86_64.rpm |cpio -idv "*.desktop"
This will extract xterm.desktop in usr in the current directory, and you
can then move it in to /usr/share/applications
You can, of course, put this in a loop and iterate over all the Packages
on the install disk, if you must.
If you have neither Fedora templates, nor the install medium, then you
can write desktop files simply enough, or get them from another user.
I should say that NOT having dom0 entries is in my opinion a good thing
- when I'm preparing Qubes for a new user I almost always delete them,
and radically simplify the menu.
unman