Any sensor activity that is sensitive to inconsistent latency, like a GPS time source. I don't think you'll find any trusted stratum 1 ntp servers using USB for clock sources.
Right, any low-latency low-bandwith application can use GPIO (or in the case of audio, isochronous USB); high-bandwidth non-latency-sensitive applications use USB.
This leaves just latency-sensitive high-bandwith applications, of which the most common is video.
