Difference between Arduino.cc and Arduino.org
The short of it is that there was a falling out within the Arduino people and now there are two groups laying claim to the "Arduino" name.

Arduino LLC runs arduino.cc. They are the steward of the Arduino IDE and libraries and own the "Arduino" trademark in the United States, and also owns the "Genuino" trademark outside of the United States. Arduino SRL (fka Smart Projects SRL) is the company that assembles(assembled) the majority of Arduino boards for Arduino LLC, runs arduino.org, and owns the "Arduino" trademark inside Italy and all of the other countries they have registered the "Arduino" trademark.

Arduino SRL recently decided that they are no longer beholden to Arduino LLC and has stopped paying licensing fees for using the Arduino name. Whether this is justified or not has not been fully tested in court yet.