See this article about Arduino DUE ADC noise:
To enhance ADC conversions, you can oversample, calibrate the ADC and average samples.
http://www.atmel.com/Images/doc11106.pdf
And some good practices when using ADC in this thread, reply #3:
http://forum.arduino.cc/index.php?topic=182446.0
Plus the AREF pin:
UOTGVBOF = USB VBus On/Off: Bus Power Control Port (PB10)
(datasheet page 1089, UOTGHS_CTRL register ):
VBUSHWC: VBus Hardware Control
0: The hardware control over the UOTGVBOF output pin is enabled. The UOTGHS resets the UOTGVBOF output pin when a VBUS problem occurs.
1: The hardware control over the UOTGVBOF output pin is disabled.