I put together a list of the places I look at for buying electronics. I didn't look at all of them, but both Adafruit and Sparkfun sell the Due: http://www.the-meissners.org/electronics.html
No, the input and output devices aren't brand specific (in fact there are few Arduino branded sensors). Note, you do need to pay attention to the voltage requirements of the device. Note, that that the Due runs at 3.3 volts, while the Uno/Mega/Leonardo/etc. run at 5 volts. Given the Due is fairly new, and uses a completely different processor underneath, there are likely libraries/devices that haven't been ported to run on the Due yet.