Comment 22 for bug 757991

I can confirm (that this is a pain).

1) Use xprops to find the proper WM_CLASS for your running application (e.g. downloaded jar, JabRef in my case).
2) From comment #16, add the proper tag to your desktop file: "StartupWMClass=<WM_CLASS>" (modify according to results of 1). This does not work yet. Actually, the app shows up for 1s and disappeared. Previously, without the startupwmclass tag, it was a void icon (nothing display), that did not work either. The trick is:
3) Put that desktop entry into your launcher, log out, log in.

I was able to hit the icon shortly before it disappeared, which crashed compiz *g*. Without compiz the icon did not disappear and right-click > keep in launcher worked fine. After relog, compiz works again and the icon too. Alternatively, it could work to drag&drop the desktop file to the launcher (which had no effect on my system - zero sized icon eventually?) and relog.