SNES9x has much better and more stable sound quality, and generally runs SNES games better, but it currently has a slight .25 seconds of input lag that can kind of ruin games on the PLAY. Once Robert gets around to finding out how to fix the lag, it's useless.
I've got Snesoid, but I'm just waiting for Robert to fix SNES9x before I really delve into my favorite SNES classics.