Broken tooth on second gear....? A freind has an Audi A4 with a vibration in fourth for that reason, it can be felt more if you pull the gearstick gently further back while accelerating in his car.
Generally speaking if it only does it in second gear then its something wrong with second, wear on other parts like mountings and propshafts is usually amplified by a lower gear but still apparent in a higher one. (hope im wrong on this one)
Try the cheapest thing first. check propshaft, driveshafts, rear shocks, rear bearings and bushes and anything else you can do for free.