What he said.
The fact is that the wall wart isn't really a regulated supply and the ATMega328P and support ICs need a 5V supply that is well regulated. All regulators consume some power. So the input to the regulator is something over 5V and everything else on the board is 5V except the 3.3V pin. The schematic http://arduino.cc/en/uploads/Main/Arduino_Uno_Rev3-schematic.pdf gives the 3.3V regulator as a LP2985 and the main regulator as a NCP1117. You can bypass the NCP1117 by providing a well regulated +5V to the Vin pin and +0V to one of the ground pins.
The main regulator is the circuit marked 117-5 (5V version of NCP1117)
