The microcontroller on the Arduino Due is specified as the AT91SAM3X8E. However, the Microchip website only documents the ATSAM3X8E microcontroller - without '91' in the name.
I browsed through the datasheet, and can't find what the '91' would stand for.
I'm thinking they changed it.
2015 datasheet still has plenty of AT91 references.
Example
Value Name Description
0x19 AT91SAM9xx AT91SAM9xx Series
0x29 AT91SAM9XExx AT91SAM9XExx Series
0x34 AT91x34 AT91x34 Series
0x37 CAP7 CAP7 Series
0x39 CAP9 CAP9 Series
0x3B CAP11 CAP11 Series
0x40 AT91x40 AT91x40 Series
0x42 AT91x42 AT91x42 Series
0x55 AT91x55 AT91x55 Series
0x60 AT91SAM7Axx AT91SAM7Axx Series