There has been some good suggestions so far.  He's my 2 cents worth.

False air leaks.  this was mentioned and DO check this out (stuff in 
archives).  your dealer said the engine ran 'too good'.  this is 
probably a reference to a smooth idle, which seems to mean over-rich 
on these engines.  

ECU grounds.  yada yada yada.  they make a difference.  find 'em and 
clean 'em up.

Plug wires.  I didn't see mention of plug *wire* replacement.  they 
go bad quickly on these engines due to high heat, road grime, and a 
Bosch conspiracy.

Spark plugs.  There are documented cases where the only difference 
between and emission failure (with new regular electrode plugs) and 
emission pass was the installation of tri-electrode plugs.  Now 
here's the kicker:  there is not a dealer listing/vw application for 
the tri-electrode plug for the 2.1L engine.  there is for the 1.9L 
and just about every vw engine in current production but not the 
2.1L.  I can't for the life of me figure out why they dropped the 
tri-electrode from the application for this engine.  They made a 
noticable difference on my 1.9L.  I really wanted to stick a set of 
tri-electrode in my 2.1L but was scared off with thoughts of 
piston-plug clearance etc.  Somebody help me out here.

Change your oil.  If your oil is real old or for some reason got 
diluted with gas, you'll get out of this world emission readings.

Exhaust system leaks.  a crack in the exhaust BEFORE the O2 sensor 
can suck in air during an exhaust pulse and make the sensor think the 
engine is lean, hence it richens itself.

Throttle switch.  oh, yes. check that puppy out.

Since a wise list member said the fruit is on the END of the limb, 
i'll go out there and say that it's NOT your ECU, basic engine, air 
flow meter or any of that other horrible stuff.  It's time to spend 
some obsessive time with the basics.  A dealer won't (and you 
probably couldn't afford it if they did) do it right 'cause it will take time 
cleaning grounds, checking for air leaks, etc.  

Hey! do you think i could start a radio show making sweeping 
generalizations like this?  Naw, nobody would ever listen to it... :)

-dan