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Although I don't yet have a vehicle of this vintage, it seems that the electronics standard moved to a new system called CAN (http://en.wikipedia.org/wiki/Controller_area_network#Automotive)
Most newer systems will give you the option to purchase OBD-II compatibility, CAN compatibility, or both in the same system.
FWIW I am currently using CarCode (http://www.obd-2.com/) and while it's not the greatest looking piece of software in the world, it does the trick.
My dad is using VOL-FCR (http://www.ilexa.co.uk/content/category/2/2/19 with his car and it seems like it can talk to more computers but costs more money?
I think the cables from each are compatible, so maybe your VW one is compatible too?
Both our cars are 1998 OBD-II.
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1998 V70 AWD->FWD Turbo 200k+
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