What is the circular gold pad on arduino mega 2560 v2 and above?
That is most likely a Fiducial Mark for the vision system of a pick-and-place assembly robot to key off of in order to more precisely place the components on their pads.

If you look carefully, you will see a second one located below the DC barrel jack.

Boards like this are manufactured in a gridded panel having a number of copies in each direction, and only cut apart after they are largely complete.  With such a large workpiece, any linearity error in the manufacturing could result in a high-density component being misplaced far enough to cause problems.  Having a pair of fiducials on each individual board in the panel can help calibrate out errors not only which might otherwise accumulate over the large dimensions of the entire panel, but also rotational skew of the panel in its holder.



You can see both on this picture of the Arduino Mega 2560 from the arduino.cc site