I have a 2010 2.5 S and I too experience this clunking sounds. After a quick browse through the manual that came with the car and a phone call to the dealer service, it turns out the sound is normal - a systems check of the the VDC (Vehicle Dynamic Control). Seriously - check your manuals - you'll see a description of the noise there.
Thank god someone said it.
Believe it or not a good portion of oem/nissan/stock/factory related questions are answered in the manual. INcluding this clunk noise that took 4 pages of complaining.
My first post! To be truthful the main reason I joined this forum was because of the, "clunk". Mine Altima is a 2011 purchased 3 weeks ago. The noise is a little bothersome but, I guess it sounds like it's normal.
This is from 5-27 for the 2011 Altima Owner's Manual. I had to search for VDC and read every instance of it until I stumbled upon this.
Quote:
"The computer has a built in diagnostic feature
that tests the system each time you start the
engine and move the vehicle forward or in reverse
at a slow speed. When the self-test occurs, you
may hear a clunk noise and/or feel a pulsation in
the brake pedal. This is normal and is not an
indication of a malfunction."