As far as I know the x3 means that the cable has 3 identical conductors, which makes it perfectly suitable for balanced use (with XLR-plugs).
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I think Peterb is right. I think the original (x1?) had one conductor/wire encased in dielectric and wrapped in shield/drain. The x2 had two conductors/wires to pass both directions of the signal (drive & drain), with shielding wrapped around the two -- for single ended (RCA) connections. The x3 had three conductors wrapped in shielding, appropriate for balanced (XLR) connections. You wouldn't expect to see x2 used for balanced or x3 used for single ended interconnects.
Great responses so far! (Keep them coming if anyone else has input!) For the record, I asked the question because my "Emerald x3" sounds better than my older "Emerald." The original Emerald is too rolled, and missing too much breath-of-life, as compared to the "x3" version. ...and this issue is a complication when we read the ads for used Audioquest cables -- we're not sure if the seller just forgot to mention the "x3" designation sometimes, or if he's just selling an older cable (that I don't want).
my understanding of this is that the x3 had an additional conductor which carried the return path signal in unbalanced mode (*or* inverting path in balanced mode), vs. the x2 which actually carried return-signal on the shield iteslf, & of course could not be used as a balanced interconnect. A call to Audioquest is your best approach to receiving an official answer to your question.