I have a 2000 Beetle 2.0, 5 spd. As I accelerate the engine chugs breifly at different times in the 2, 3, 4 and 5th gear. Any idea's?

could be anything, engine check light on?
Most likely fuel delivery or ignition. Depending on how many miles you got, could be fuel filter or injectors, or could be spark plug wires or the plugs themselves...