I've never really seen anything other than USB, but I haven't used much in the way of desktops/towers in years, just laptops.

I also experience noise issues with USB fairly regularly....not sure exactly why. But static and such, especially it comes through when using the trackpad.

My solution, which definitely works but I'm not sure why, is to use a topping ds10. This is still USB input, but it has optical and spdif output in addition to analogue. So I have USB to the ds10 and use the digital output to my DAC and it's clean as a whistle.

So, I guess it's a combination of USB and OPT/SPDIF for me.