In my current setup I have both the s/pdif and toslink output from my sound card (E-Mu 1212M) going to my DAC (Benchmark DAC1). The DAC1 provides a switch on the front that tells it which input to use, and I frequently find myself A/Bing between them to see if I can hear any difference. I've tried A/Bing between them while blind, with my wife switching it while my back is turned, and not blind, when I hear some problem in the music and I'm curious if it disappears with the other digital input...these are invariably problems in the original recording, verified by playing the CD on another system using the original CD.
So, I can't hear any difference between s/pdif and toslink in my current setup.
I often flip-flop about which input I want to use (optical is better from a computer, but coax is supposed to sound better, but my optical cable is supposed to be really good, but so is my coax cable, and so on) and have gotten to the point where I usually don't even know which one I'm using.
In the past, I found that coax sounded better (with a different set of cables...eBay glass vs. Elco UDC-S), but occasionally the coax setup would cause errors on my DAC1 (the red light would flash), usually when Windows was trying to play a sound on top of the ASIO output of Foobar. I am pretty sure this was a problem with the E-Mu drivers...however, I believe it is fixed now with their latest drivers...I haven't seen a red light flash on my DAC1 with coax input in a long, long time, even when playing a game like World of Warcraft with the sound on for hours while simultaneously playing FLACs with Foobar2000 using ASIO output.