According to the manufacturer of my mobile device, Flight Mode kills all transmitter/receiver circuits inside of the phone. Along with the internal transmitter, all superhets and radio related local oscillators are shut down, including bluetooth and 3G/Data.
I have been assured that the company's phones, when in flight mode, produce weaker and far fewer spurious signals than your average laptop does in lab tests covering comparable bandwidths.
That said, I have personally observed and have been informed by people I trust regarding the numerous and various odd effects a powered up cell phone can have on avionics - often without even being in a call.