Some sources of audio may be played via a background process or simply not be displayed in the list of sources. Some examples would be a Dashboard Widget like the BBC Listen Live Widget or the open source MPlayer.
Hold down the option key when you click on the the source popup menu in WireTap Studio to see all of the possible capture sources listed. This works on the popups in the preferences as well. You will notice that there are a lot more things listed, including the ones you are looking for.