I make the choice based on the number of open slots - if you can, avoid using the last slot. The reason is that some devices offer optical, some coax, and some both. So if you have a device that offers both and you have 3 open optical and 1 open coax inputs on your receiver or pre/pro, I would advise choosing optical.
Of course, you could always juggle around the cables if you ran into a problem, but it would be nice to avoid the hassle.
The digital information is sent out encoded as analog along with the clock information. So there will be some error correction and jitter going on to various degrees with different digital cables. And hence slightly different sound with different cables.
I have found the 'Glass Toslink' optical cable listed on audiogon.com for $30 to be very good, even when compared to some high end digital coax cables. Go for it.
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