I've read on-line that this is a problem with a questionable fuel dampener. I don't know the mechanics of it, but it seems that replacing it fixes this problem in a lot of Toyota/Lexus cars. I've been having a similar problem, but drive the car so seldomly right now (transmission noise) that I haven't tried it yet.
The fuel dampener is a little device on the inlet side of the fuel rail. It's purpose is to dampen the pulses from the fuel pump as the fuel enters the rail. It looks like a small vacuum motor with no lines running to it. You can feel the set screw vibrate (under the dust cap on top) when the car is running, smoothing out the pulses. I'm guessing that it gets weak and begins to allow fuel pressure variations that muck with the low-speed smoothness.
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