But most motherboards have SPDIF on them stock, right? So what exactly does a sound card bring to the table?
Convenience, price and equipment efficiency. If you have a decent power supply unit coupled with a high-end sound card like a Xonar STX, you have the convenience of an all in one package installed in your desktop that you can, for a reasonable price, attach your headphones to with no extra boxes taking up limited desktop space. Very nice.
Now if one gets the sound quality bug, the sound card then becomes a conduit one can extract HDD stored music files from and via the S/PDIF out, the better DAC/Amp combination takes over.
So it all boils down to price, convenience, desk space and finally, overall, what the listener wants out of the deal.