The ATmega16U2 (or 8U2 in the rev1 and rev2 boards) firmware source code is available . The ATmega16U2/8U2 is loaded with a DFU bootloader, which can be activated by:
On Rev1 boards: connecting the solder jumper on the back of the board (near the map of Italy) and then resetting the 8U2.
On Rev2 or later boards: there is a resistor that pulling the 8U2/16U2 HWB line to ground, making it easier to put into DFU mode.
You can then use Atmel's FLIP software (Windows) or the DFU programmer (Mac OS X and Linux) to load a new firmware. Or you can use the ISP header with an external programmer (overwriting the DFU bootloader). See this user-contributed tutorial for more information.