In TLDC, you can either define your own applications, or use apps (.desktop files) already on the system. However, for the meny structure, you cannot re-use existing .directory files. I think you should be able to to that; the existing files already have the correct icons, translations etc.
On my F11 system, the files are in /usr/share/desktop-directories/. However, it's not possible to simply copy them to /opt/thinlinc/desktops/xdg_data_dir/directories/thinlinc, because all available menus must also be listed in tl-desktop-customizer.hconf. I wonder why, this seems a little bit un-SPOTy.
After implementing this bug, we can probably get rid of the default shipped structure, as will be implemented by bug 3200.