The difference between Atmel ATmega16u2-MU and -MUR
According to Digikey: http://www.digikey.com/product-detail/en/ATMEGA16U2-MUR/ATMEGA16U2-MURCT-ND/2477167 the "MU" parts are packaged in a tray while the "MUR" parts come in Tape-and-Reel (or cut tape). Refer to the bottom right of the linked page under "Alternate Package".