I thought one of the fuel injectors might be clogged. First, I hooked an oscilloscope to each of the injectors to see what the signal looked like. Each one had an identical signal - 50V for .16ms, followed by a rapid voltage drop for the next .24ms. I then unplugged each injector in turn to see if maybe one didn't have an effect. Each slowed the idle slightly. However, I noticed a whistling when I unplugged the cable from one. I found that when I wiggled it, it seemed to be leaking. I used a mechanic's stethoscope to verify that there was a leak on #3. I also found a small leak on #6. That was odd, because I had replaced all the o-rings just a few months back.

I replaced the o-rings again ($21 - ouch), plus rotated the injectors to different cylinders to see if the problem moved.

Success! The idle is no longer rough, and the check engine light has not come back on. I'm a bid dubious that this is the entire problem - I won't be surprised that it comes back on in a few weeks.