Hey! I've got the same problem (1994 6sp tt)... sometimes the car will idle very low, around 400-500. The problem goes away after restarting the engine, doesn't it? The engine may sometimes eaven die and after a restart the idle is just fine.. that is, about 200rpm higher.
Actually it seems that the car can be in either one of these two modes after its started:
with 90% probability 1) normal idle, everything is nice and smooth
with 10% probability 2) extremely low idle, the car may eaven die
I've changed plugs and coilpacks because of ignition problems that i had earlier.. The ignition is fine now but it didn't affect this problem. The idle is perfect when the car chooses to idle at ~650 .. no misfires or wandering at all.
(note: i've got s-afc 2 + vpc installed, but i don't think it has anything to do with this)