I have used versions of Yamaha's YPAO calibration system for a few years now, and I really find it to be very useful for room calibration. With YPAO you can run the auto setup feature, then manually adjust or fine tune any aspect of it. So I'll typically run YPAO, letting it setup speaker distances, size, LFE cutoff, etc., and then I will fine tune those settings with my SPL meter.
I've been really pleased with the results. The drawback with Audyssey is that since it's 3rd party and licensed to manufacturers, the extent to which each receiver allows you to modify the settings can be limited.
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