Piotr wrote a post on his blog about using some of advanced capabilities of ADC in Arduino Due:
Today I’m going to present some of more advanced capabilities of ADC built in ATSAM3X8E – the heart of Arduino Due.
I like the Arduino platform. It makes using complex microcontrollers much simpler and faster. Lets take for example the analog-to-digital converter. To configure it even on Atmega328 (Arduino Uno/Duemilanove) you must understand and set correct values in 4 registers. And it can be much more in complex device, like 14 in ATSAM3X8E (Arduino Due)!
Playing with analog-to-digital converter on Arduino Due – [Link]