It's also oftne used when you are travelling internationally, and taking a second flight after you arrive at a gateway city.

Coming from Europe to the States, for example, you have to go through passport control/immigration, then collect your bags and take them through customs and make your declaration.

The transfer desk is where you would recheck your bags on the domestic side and get your new boarding pass if necessary. Then you're done with all the formalities for the rest of the trip.