Gentlemen: I'm a microwave scientist and the killing of bacteria using microwave energy has been demonstrated many times as due to thermal heat; there is no "microwave effect" (the quantum energy content of microwaves is lower than that of light!) - this appears over and over in peer-reviewed publications.
I need to correct a misunderstanding that appears in the first reply: "I understand that the microwave frequency is designed to be compatible with the resonant frequency of water molecules." This is not true. The resonant frequency of water at 25 C is 22 gigahertz (GHz); the microwave oven frequency is 2.45 GHz - so the efficiency of energy conversion is poor - in fact water is majorly a reflector. Further, as water gets hotter it's resonant frequency rises, while that of the microwave oven remains the same. Therefore, the water absorbs and coverts microwave energy into heat less efficiently as water becomes hotter This is a good thing since it acts as a moderator to control the rate of heating. Try a simple experiment: take three 600 ml beakers, add exactly 500 grams of water to each where the water is either 10, 20 or 30 C (measure and record this starting temperature). Microwave one at a time for exactly 60 seconds and measure the final temperature. Compare it to that sample's starting temperature and you'll see that the coldest water showed the greatest temperature rise.
Another important thing: when salt is present another heating mechanism, ionic conduction, dominates - in this case, the salted water or food (ham for example) heats faster the hotter it becomes - a phenomenon known as thermal runaway - extremely difficlut to control - it may lead to fires in some material.
