Between my BDP-3 and BDA-3, I've gotten the best sound quality using USB. I've delved into this a few times recently, out of renewed curiosity. The BDP-3 is serving music files from a WD NAS drive and via a local router output, connected with a fairly standard network cable.
I specifically compared this to the AES/EBU connection, using a Mogami XLR interconnect that has been giving very good sound quality for analog interconnections (discovered a couple of months ago). To my surprise, there was no contest, in favour of the USB. The Mogami 3173 is spec'd as a constant impedance suited to AES/EBU.
A couple of other experienced listeners have heard this Mogami 3173 compared in my active T10 system, and both agreed. One has ordered sets to connect his BAX1 to his amp channels in an active system using Model Ts.
Brian