A problem with the ball joints can cause a creaking noise. There is an updated part to remedy this problem.
Car Problem Reports
Mercedes-Benz R350 Problem With Ball Joints May Cause Creaking Noise
Mercedes-Benz R350 Problem
Average Mileage: 73,125 mi (52,000 mi - 100,000 mi)
Visitor, 2007 Mercedes-Benz R350, 52,000 mi
Creaking rear ball joints
Visitor, 2006 Mercedes-Benz R350, 66,000 mi
when stepping on the break the axle under the car makes a creaking noise.
Visitor, 2006 Mercedes-Benz R350, 76,000 mi
RECENTLY PURCHASED NOTICED SQUEAKING WHILE DRIVING IN ENCLOSED AREA LIKE GARAGE STILL NOT FIXED LOOKING FOR MECHANIC
Front & rear creaking sounds first occurred 65K miles. Creaking/squeaking over bumps and heard creaking when getting in and out of car. Leaky struts / shocks needed replacing. Rear creaking cause unknown and persists to date (95K miles).
Visitor, 2006 Mercedes-Benz R350, 54,000 mi
Same creaking noise as others have said.
Visitor, 2006 Mercedes-Benz R350, 84,000 mi
Clunks and/or pop when letting of the brake or turning when forst moving the car.