Another factor, also subtle but reliably reproducible: if the stereo has been off for a couple of days, it sounds worse when I first turn it on, for a couple of hours.

My guess(?) is that warming up the voice coils, by running current through them -- or possibly keeping the surrounds loosened up by exercising them? -- makes the speakers more accurate. To that end I've taken to turning on Pandora when I go to bed at light, and closing the music room door (which is pretty much sound-proof.)