Second, before I actually state my reasons, let's talk about how microwaves work, shall we?
How Your Microwave Actually Heats Your Food:
Microwaves are a form of electromagnetic radiation—waves of electrical and magnetic energy moving together through space. EM radiation ranges from very high energy (gamma rays and x-rays) on one end of the spectrum to very low energy (radio waves) on the other end of the spectrum.
Microwaves are on the low energy end of the spectrum, second only to radio waves. They have a wavelength of about 4.8 inches—about the width of your head.
Microwaves are generated by something called a magnetron (a term derived from the words “magnet” and “electron”), which is also what enabled airborne radar use during WWII. Hence the early name for microwave ovens: radar ranges.
A magnetron is a tube in which electrons are subjected to both magnetic and electrical fields, producing an electromagnetic field with a microwave frequency of about 2,450 megaHertz (MHz), which is 2.4 gigaHertz (GHz).
Microwaves cause dielectric heating. They bounce around the inside of your oven and are absorbed by the food you put in it. Since water molecules are bipolar, having a positive end and negative end, they rotate rapidly in the alternating electric field. The water molecules in the food vibrate violently at extremely high frequencies—like millions of times per second—creating molecular friction, which heats up the food.
If the food or object place in the microwave had no water it would not be able to have this resonance heating type effect and would remain cool.
Structures of the water molecules are torn apart and forcefully deformed. This is different from conventional heating of food, whereby heat is transferred convectionally from the outside, inward. Microwave cooking begins within the molecules where water is present.
Contrary to popular belief, microwaved foods don’t cook “from the inside out.” When thicker foods are cooked, microwaves heat the outer layers, and the inner layers are cooked mostly by the conduction of heat from the hot outer layers, inward.
Since not all areas contain the same amount of water, the heating is uneven.
Additionally, microwaving creates new compounds that are not found in humans or in nature, called radiolytic compounds. We don’t yet know what these compounds are doing to your body.
In addition to the violent frictional heat effects, called thermic effects, there are also athermic effects, which are poorly understood because they are not as easily measured. It is these athermic effects that are suspected to be responsible for much of the deformation and degradation of cells and molecules. 
My Reasons for NOT Using the Microwave:
*Questionable: Moms (and nurses and leche legue leaders) out there will tell you NOT to microwave breast milk. Why? Because it destroys the nutrients, kills essential amino acids and negates B12. If it can that to breast milk, why would it not effect other food? It has also been shown to kill the good microbacterial spores in honey (you know, the stuff that makes honey so good for you?).
*Although I use very little plastic, it is an argument out there: Carcinogenic toxins could be leached from plastic or paper plates or covers and mix with your food. See my post on BPA.
*A study published in the November 2003 issue of The Journal of the Science of Food and Agriculturefound that broccoli nuked in the microwave with a little water lost up to 97 percent of the beneficial antioxidant chemicals it contains. By comparison, steamed broccoli lost 11 percent or fewer of its antioxidants. (Again, just another one of those studies that you can disregard if you are inclined).
*Perhaps the most concrete evidence of the dangers of microwaves comes from Dr. Hans Hertel, a Swiss food scientist, who carried out a small but high-quality study on the effects of microwaved food on humans. His conclusions were clear and alarming: microwave cooking significantly altered the food‘s nutrients enough so that changes occurred in the particpants‘ blood--changes that suggested deterioration. The changes included:
- Increased cholesterol levels
- More leukocytes, or white blood cells, which can suggest poisoning
- Decreased numbers of red blood cells
- Production of radiolytic compounds (compounds unknown in nature)
- Decreased hemoglobin levels, which could indicate anemic tendencies
*Microwaves are used in the field of gene altering technology to weaken cell membranes. Scientists use microwaves to actually break cells apart. Impaired cells then become easy prey for viruses, fungi and other microorganisms.
*Some "studies" have found that the microwaves actually turn molecules into carcinogens (aka cancerous).
*In the end, I would just rather be safe than sorry. We honestly don't know what microwaves do. And it really isn't that inconvenient to reheat my food using the stove or oven. I actually find myself eating more fruits and vegetables for lunch at work because I don't have the "reheating leftovers" option. Win-win if you ask me.
Other "studies" you can learn more about:
- A 1999 Scandinavian study of the cooking of asparagus spears found that microwaving caused a reduction in vitamin C .
- In a study of garlic, as little as 60 seconds of microwave heating was enough to inactivate its allinase, garlic’s principle active ingredient against cancer .
- A Japanese study by Watanabe showed that just 6 minutes of microwave heating turned 30-40 percent of the B12 in milk into an inert (dead) form . This study has been cited by Dr. Andrew Weil as evidence supporting his concerns about the effects of microwaving. Dr. Weil wrote:
- A recent Australian study showed that microwaves cause a higher degree of “protein unfolding” than conventional heating.
- Microwaving can destroy the essential disease-fighting agents in breast milk that offer protection for your baby. In 1992, Quan found that microwaved breast milk lost lysozyme activity, antibodies, and fostered the growth of more potentially pathogenic bacteria .