If you want to be able to mod the hell out of it and get tons of power and still get milage go 1.8t. If you want lots of torque and only a limited selection of mods without adding a turbo or supercharger go vr6
It all depends what you want out of your engine and how / where you drive.
If you read up on the 1.8T vs VR6 thread, it'll give you many many points of debate to consider.
Please read it over entirely first and then you can ask specific questions if they come up.
* http://forums.vwvortex.com/zerothread?id=1839444
- Erik
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