My 300E does that too! I have a slight incline out of the driveway in the morning, and when I coast down and press the brake, I get an additional "clunk" with a noticeable added pedal travel.
Did it since I purchsed it three years ago (@ 72K). Service tech said all is normal, and the problem hasn't worsened. Brake pads have been serviced twice over the course of my ownership, but the "clunk" is still there.
I'm not about to worry about it, unless the "clunk" is followed by other noises...like little metallic sounds of brake parts rolling down the driveway...
2009 ML350 (84K) - Family vehicle
2001 CLK430 Cabriolet (71K) - Wife's car
2005 BMW 645CI (124K) - My daily driver
2012 Mustang V6 (60K) - Daughter's car