The following instructions can be used to restore the 16u2 firmware on an arduino mega2560, rev 3. Using a Macintosh/osX (Lion), with the Arduino IDE 1.0.0 installed in the applications folder.
1) Plugin a usb cable to the arduino mega rev3 in order to supply it with power.
2) Plugin an avrispmkII programmer into the 6 pin icsp1 jack located adjacent to the usb connector (observe pin1 orientation via the dot on the board). I had to use an 'extender' for the icsp1 connector as the avrispmkii connector wouldn't fit due to proximity to one of the edge-connectors on the arduino.
3) Open a terminal window, paste in the following command and execute it:
/Applications/Arduino.app/Contents/Resources/Java/hardware/tools/avr/bin/avrdude -C /Applications/Arduino.app/Contents/Resources/Java/hardware/tools/avr/etc/avrdude.conf -p m16u2 -F -P usb -c avrispmkii -U flash:w:/Applications/Arduino.app/Contents/Resources/Java/hardware/arduino/firmwares/Arduino-COMBINED-dfu-usbserial-atmega16u2-Mega2560-Rev3.hex -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0x0F:m
4) Unplug both the programmer and the usb cable, then plug the usb cable in and the mac (and the pc) should recognize the usb port.