The flight crew of a Republic Airways Embraer 170, operating as United Express flight 3417, said they had stopped their airplane and set the parking brake while waiting for gate personnel to finish preparing gate 88 at Newark Liberty International Airport (KEWR) to receive their flight, when their airplane was struck by a Turkish Airlines Airbus A330 that was taxiing past. The Embraer airplane received substantial damage to the rudder and vertical stabilizer. The captain of Turkish Airlines flight TK0029, said that after landing they were cleared to taxi to gate 63, and while taxiing on Taxiway A, there was an airplane stopped on the right-side apron. The captain said that no information had been relayed that an airplane had stopped short of the parking area, and he slowed his taxi speed, but did not realize that the stopped airplane had not fully pulled into and parked at the gate. He perceived that there was sufficient clearance, so he decided to pass. After reaching gate 63 and parking he said that he was informed of the collision. An inspection of the A330 airplane revealed paint transfer on the right winglet.