apparantly the woodgrain panels are a problem, my drivers side door pull is cracked like crazy with sections missing and the passenger side is cracked as well.
i've also read about problems with the maf sensor although many people have had success by cleaning it with 99% isopropyl alcohol/electrical contact cleaner/maf sensor cleaner (which you can pickup from supercheapauto for around $20-25). i picked mine up with 105k on the clock and have had no issues.
the glovebox latch is also a problem so keep an eye out for that.
the window regulators were also a problem. i looked at my 02' model due to a fault with the lock module (also a problem) and it had metal clips, i can't say whether this was fixed model-wide or if mine was replaced during a service.
i don't think there are too many other mkiv gti specific problems though, just general things like service history including timing belt change. speaking of which the water pump is also a possible cause of concern as they came standard with a plastic impeller which i think was fixed in later mkiv's.
i've racked up almost 2500k's since purchasing it and apart from a rough idle which was fixed by cleaning the throttle body and adjusting it via vagcom (it's worth getting a vag com cable off ebay as well as a copy of vcds lite), i've had no other mechanical problems so far *knocks on wood*.
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