What is this on top of the Air Force One?
The aircraft is the Boeing E-4B Advanced Airborne Command Post 'Nightwatch', which serves as the survivable mobile command post for the US National Command Authority. The aircraft are based on the same Boeing 747s as the VC-25s used by US President.
There are four identical aircraft performing this function in the US. The &quot;bulge&quot; on the top is a radome that houses a steerable SHF SATCOM antenna, as can be seen in the following image.

Image from cnet.com
The following image shows the aircraft systems in a little more detail.

Image from http://everythingisahoax.tumblr.com
As a side note, Air Force One refers specifically to USAF aircraft carrying the US President. From US DoT ORDER
JO 7110.65W 

When the President is aboard a military aircraft, state the name of the military service, followed by the word &quot;One&quot;.
EXAMPLE−
“Air Force One.”
“Army One.”
“Marine One.”

For civil aircraft, it is Executive One.