I've heard that even though the gas comes in from the bottom of the tank, the junk floats at the top. When you are running low on fuel, the top of the tank and the bottom of the tank get really close together, thus you are more likely to get a clog. In addition (I'm not a mechanic) I've heard that the fuel pump has to work harder (less pressure) when there is less fuel in the tank and (a traditional gasoline engine) can hesitate when accelerating. I notice that my car does this a lot when I am running low.
Short of trying to get into the 700 mile club (the mile high club is a better accomplishment) I'd advise against running the car with an empty tank. Remember, I am not a mechanic.