Steam keeps all shortcuts on a file named "shortcuts.vdf", that sits on the 'Steam\userdata\<userid>\config' folder.
Recently, I lost mine as well. That file had 0 bytes. HOWEVER, for some reason I'm not aware of, Steam placed a copy of it on 'Steam\config'. I just copied that version over to 'Steam\userdata\<userid>\config' and my non-steam shortcuts were back after a Steam restart.
now, from time to time, I just backup that file on 'Steam\userdata\<userid>\config'
I don't really remember if it happened exactly like that or if it's the other way around. Anyway, check both folders and, if you're lucky, a valid copy of your 'shortcuts.vdf' will be in one of these folders. Just copy it over to the other folder and restart.
I first read about it on this thread, so maybe they can explain better than I can:
http://forums.steampowered.com/forums/showthread.php?t=2546782
Maybe Valve should just save that file on the cloud....