It could be a number of things including shock absorbers
This is known as the "dead body in the trunk" sound. A number of owner's have reported this sound particularly on the W211 chassis. Kent explains what he did to fix it in this 2004 E500 sedan. The same problem can happen on other models as well, even without the airmatic suspension.
Problem & Solution
Common among these chassis:
R107
W108 W109
W110 W111 W112 Sedan
W111 W112 Coupe
W113
W114
W115
W116
W123
W124
W126
R129
W140
W201
W202
W208
W210
W211
W220