Capacitors on Arduino Due
The datasheet for the Atmel ATSAM3X8E Microcontroller used in the Arduino Due specifies the following about bypassing and stabilizing VDDOUT:


  To ensure stability, an external 4.7 µF output capacitor, CDOUT must
  be connected between the VDDOUT and the closest GND pin of the device.
  The ESR (Equivalent Series Resistance) of the capacitor must be in the
  range 0.5 to 10 Ohms.
  
  Solid tantalum, and multilayer ceramic capacitors are all suitable as
  output capacitor. 
  
  A 100 nF bypass capacitor between VDDOUT and the closest GND pin of
  the device decreases output noise and improves the load transient
  response.


From Table 46-3 of the "SAM3X/SAM3A Series Complete" datasheet

The capacitor value specified for stabilizing / decoupling a power input or output pin in datasheets is typically a minimum, indicative value - If there is also a maximum acceptable value, that may conceivably be separately specified. 

Electronics designers often use a higher value capacitor within the same order of magnitude, if they foresee a high load on the power rail - The higher the capacitance, the better it is able to weather out load-related ripples on the power rail. 

The upper practical limit on this capacitor value is set by the initial power-on current that would be drawn from the power pin to charge this stabilizing capacitor - Too high, and the supply may be damaged.

The (optional) 100 nF capacitor specified for bypassing, is for the purpose of providing a short-circuit path to ground for any high frequency noise on the power rail. This is placed in parallel with the stabilizing capacitor, both as close as possible to the power pin concerned. 

That is why you see the 10 µF and 100 nF capacitors in the Arduino Due reference schematic.