And so the shield compatibility problem begins. Note the first sentence in the below, does that sound like a beginner might think any present should he might own will work ok with the new Due? Later it tries to explain that all shields may not indeed work with a Due or some can even cause damage, but it's certainly not a crystal clear to this reader what is trying to be explained. However this a article from Wired so not sure if the source is from Arduino or just the writers attempt at an explanation? Anyone ever see an official arduino R3 spec? I don't recall seeing one published, although I'm assuming they means new shields should have that mating connector pin and read the voltage present on the new IOref pin to determine is it's a 3.3vdc signal meaning the controller the shield is attached to is operating at that voltage. Older controllers will not have that pin so no voltage will be sensed by a connected shield board.
The Due will continue to work with all Arduino shields — add-on boards and circuitry like motion sensors and LED light arrays — that conform to the official Arduino Revision 3 layout. However, the Due operates at 3.3V whereas AVR-based Arduinos operate at 5V, meaning some third-party shields that don’t follow the R3 specs to the letter may not be compatible, depending on their voltages. It also means those looking to use the Due in existing applications should adjust their voltage or risk damaging their board.