AES EBU standard hypothetically should be higher grade than other spdif output. Its cable suited for longer runs. In proper implementation, I find it to be the same as coax for connecting equipment on the same rack.
I dont believe in cables; i just have regular off the shelf blue jeans stuff. I used to believe that SPDIF should all be the same and that digital was digital until i started going to meets and playing with different combinations. I personally believe that the digital receiver sections of the Gungir and Yggdrasil DACs are gimped and some corners were cut in their implementations. I think both DACs sound much better when my y3 is between (USB and ERC-3).
I perceive differences in USB and SPDIF (try it for yourself CD transport i.e. PS3 vs USB) If you think you can hear a difference let me know. Based on my ears AES/Coax sound the best, toslink, and then USB.
The best USB implementations that i have heard sound clean, but lean and/or sterile compared to the other inputs. You could spend a lot of money on USB rabbit hole, so i just decided to go back to physical CD media/transports.
I personally avoid using USB if possible at home, but when i use it - Foobar2000 (primarily for the remote control/server functions, plus it integrates with my NAS a lot better). I tend to use the y3 as a dedicated USB transport/decrapifier/digital receiver when i'm not using it as a DAC.
The y3 has an Atmel based USB (UAC1 & 2) receiver with custom audio-widget firmware (open source). It's has its own dedicated LPSU, galvanic isolation, and i2s isolation. Surprisingly for an open source board, i have had the least driver issues in windows compared to CMedia based products. The ERC-3 and physical CD's are my main source.
If you really insist on going down the usb nervosa path, check out the really well designed products - offramp5 and Berkeley audio alpha usb (don't mind the prices). Then check out the singer su1.