Quick update... I ended up buying a Sherwood Newcastle R-972 from Accesories4less, which I've had for a little over a week now. The sound quality is noticeably better than what I heard from the Onkyo HT-R540 even without any room EQ.
I'm wary of the descriptions people write about new equipment, but I'll give in for a moment: on some of our favorite songs (e.g., Diana Krall's East of the Sun), the music sounds more detailed and present. I heard this during A/B testing when I first setup the 972 (though not blind and switching required physically moving the cables). Then I took a week to get used to the new unit and switched back over the weekend. The 540 sounded muddy and Diana's voice was lower (not in a good way), almost like the whole frequency range had been smushed together a bit. That said, it's not like the sound from the 540 was *bad*, but the improvement wasn't subtle.
Since my first post, I've been out listening a couple times. The best speakers I've heard so far (in our price range) are the DynAudio Excite X16s, though I'm finding it very difficult to compare speakers since most stores seem to have poor listening environments. I'm hoping to find a way to listen to the philharmonics (anyone in LA? I'll bring beer) since the X16s are nearly the same price.