I solved it for ukki's Knots Ruby application: Use xprop to get the WMCLASS of your program and add StartupWMClass=<WMCLASS as given to you by xprop> to your desktop file.

Thanks a bunch, I'll try.

Actually, I found the way ruby binding deals with the window class and window title - a bit strange. It puts the window class as the first part of the window title (second part is what you give to set_title)