I have a 2002 RX300 w/ 55K miles and experience something similar... to me it seems like a low-frequency harmonic resonance sort of thing. I hear it only while the vehicle is stationary, idling and in gear. Shifting to park or neutral eliminates the noise. There does not seem to be any roughness to the motor, just this low frequency sound resonating in the car.
At first I wondered if it was an exhaust problem, but now I've been wondering if it is related to the transmission somehow? Much more of the transmission internals are engaged while in gear. Clutches, valves, etc are active that are idle when in park. I'm wondering if changing the tranny fluid will make any difference.
I've also found that I cannot hear the noise if I significantly rotate the stereo volume knob in a clockwise direction..
