I have not done any critical listening comparing toslink, coax, and XLR connections, but from everything I know, I would avoid a toslink connection, particularly a long one. -J
For long runs, I had bad luck w/toslink... Just sounded cloudy. I use an Edirol UA-1D, which converts USB to coax with a looooong USB run and a short coax run to my Theta DAC.
I have not tried the Apogee, but do have the Benchmark with a PC set up. I am using an RME card with an AES/EBU balanced link and it sounds great. The Benchmark is so jitter resistant (and the RME has really good jitter specs) that I don't think I would gain anything going to USB. The balanced connection can also be run much further than a coax or toslink. Even the analog output of the RME card is surprisingly good. - J
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