There are downsides to all three methods. If you shut the car down by pinching the fuel line, you run the engine lean temporarily. If you shut the engine down by bumping the flywheel, you are putting stress on the engine internals from the sudden stop. If you plug the exhaust, I have heard that it can send pipe ooze (which contains metal flakes, dirt, carbon and spent oil) backwards into the engine.

EDIT: If I am near where I keep my starter box when the car needs to die, I use my engine stopper (which plugs the pipe). If I am not, and the engine is idling, I pinch the fuel line. If its a runaway and running wide open, I stick the tip of my shoe against the flywheel.