At approximately 1550 central time, a Rockwell 690B suffered the loss of the top portion of its rudder while in cruise flight at 16,000 feet near New Braunfels. The flight landed without further incident and none of the three aboard was injured. The plot reported that the gear-in-transit light was on for the duration of the flight but he continued the flight. While cruising on autopilot, the pilot noticed the ball was not centered. He adjusted the rudder trim and a couple of minutes later the airplane began violent shaking an yawing. The airplane rolled into a 70-degree left bank and pitched 10 to 15 degrees nose-down. He recovered the airplane and continued to his destination. During the descent the ball was fully deflected to the right. Post-flight examination revealed the top eight to 10 inches of the rudder was missing, the rear of the fuselage was wrinkled and the left gear door was bent back 90 degrees.