MCU Type ATmega16U2 not avaliable in Eclipse AVR Plugin
The ATmega16U2 on those boards isn't intended to be programmable by the end-user. It's only there to help convert from USB to TTL serial, which lets your computer communicate with the board's main microcontroller. It replaces the FTDI chip which was used on some older boards.

In the case of the Uno, the main microcontroller is the ATmega328. For the Due, it's the AT91SAM3X8E. If you want to program them from the Arduino IDE, you can usually just select the board by name from the drop-down menu.