I've never run out of gas but once ran out of diesel. The Cummings guy warned me that injected engines that run out of fuel can sometimes have problems with air pockets in the lines when new fuel comes in. Much like a water faucet spurts when the main water is shut and then opened in your house.
I would imagine this may also be true of gasoline engines. If your injector system has air pockets, you will get a rough running engine.
I would suggest avoiding the empty tank condition at all costs. These aren't 9N tractors we are driving.
roadster with a stick