What is manual muscle testing and applied kinesiology and why should I care?
Manual muscle testing (MMT) is a method of using the strength and response of a muscle to test function in the body. Applied kinesiology is an art more than precise method of using a manual muscle test to evaluate a condition in the body. Applied Kinesiology (AK) is a system that evaluates structural, chemical, and mental aspects of health using manual muscle testing combined with other standard methods of diagnosis according to the International College of Applied Kinesiology.
A brief history of manual muscle testing and applied kinesiology:
Manual muscle testing was developed in 1915 by Robert W. Lovett, MD as he was trying to determine muscle weakness in polio patients. Then in the 1940's Henry and Florence Kendall published a book called “Muscle Testing and Function” which defined specific muscle tests to isolate each specific muscle. Frank Chapman, DO first described small tender nodules just under the skin that he related to dysfunction of an organ system in the 1920's.  These small tender nodules are called Chapman's reflex points or neurolymphatic points as they are referred to in AK. Dr. George Goodheart was a chiropractor who practiced in Michigan and the founder of AK. Dr. Goodheart published the Applied Kinesiology Research Manual in 1964. He made many observations when conducting muscle tests developed by the Kendalls in association with Chapman's neurolymphatic points. Dr. Goodheart noticed certain muscles were related to Chapman's neurolymphatic points. This correlation is used in AK to indicate an organ that may be stressed. A chiropractor named Terrance Bennett identified points in the body that he related to the circulatory system which he called neurovascular reflex points in the 1930's. These neurovascular reflex points are also related to specific muscles. AK utilizes acupressure meridian points and the flow of cerebrospinal fluid in the treatment of dysfunction. Although all four of the previously mentioned methods are used in AK the primary method of treating a dysfunctional or “weak” muscle is through chiropractic adjustment.
How is muscle testing used?
“… MMT may not be just testing for actual muscle strength; rather it may also test for the nervous system's ability to adapt the muscle to the changing pressure of the examiner's test. activity to meet the demands of the test. ”  There are several factors that can affect a muscles response to a manual muscle test. These may be structural (dealing with the nervous system), lymphatic, dealing with the vascular system, cerebrospinal fluid flow, or the acupuncture system. The goal of applied kinesiology and the manual muscle test is to address the root problem in the body. The chiropractic adjustment is the primary and initial treatment when using AK. There are times when a chiropractic adjustment fails to resolve the issue. AK can then be used to further evaluate the body to determine if a stressed organ or body system is the problem.
According to a study published in 2008 in the Journal of Chiropractic and Osteopathy a “reason for the addition of manual muscle testing to chiropractic diagnostic methods is that most other parameters of dysfunction identified in low-back and neck pain patients have not been shown to precede the pain, but rather only to accompany it. “An important exception is muscle strength, which can predict future low-back and neck pain in asymptomatic individuals.” 
Pain is an indicator that there is a problem in the body. Pain is a symptom though and not the underlying problem. Addressing the underlying problem is the only way to move the body towards correct function and away from dysfunction. Muscle weakness and imbalance is a much better indicator of dysfunction in the body than pain.
What else may a muscle test be telling me?
As mentioned earlier there are several factors that can affect a muscle's response to a muscle test. There has been shown a correlation between weakness in certain muscles and problems in an associated organ. A study published in the Journal of Manipulative and Physiological Therapeutics in 2004 reported a case of a young man with low back pain which could not be resolved through oral anti-inflammatory agents or local cortisone injections. The patient then tried Chiropractic adjustments which were not resolving the issue. Throughout AK evaluation the author was able to identify a congenital large intestine abnormality which the patient forgot to identify initially. This abnormality was the root cause of the young man's low back pain. After properly addressing the large intestine the back pain subsided. 
Manual muscle testing and applied kinesiology are methods of evaluation that are used in conjunction with other more typical diagnostic tools to determine the cause of dysfunction in the body. The body has a very powerful ability to heal itself when given the opportunity. The cessation of pain and identification and removal of dysfunction increases the body's ability to heal itself.
1. Chapman reflex points. (nd). Retrieved October 19, 2015, from https://en.wikipedia.org/wiki/Chapman_reflex_points
2. Cuthbert, SC, & Goodheart, GJ (2007). On the reliability and validity of manual muscle testing: A literature review. Chiropractic & Osteopathy Chiropr Osteopat, 15 (1), 4.
3. Schmitt, WH, & Cuthbert, SC (2008). Common errors and clinical guidelines for manual muscle testing: “the arm test” and other inaccurate procedures. Chiropractic & Osteopathy Chiropr Osteopat, 16 (1), 16.
4. Caso, M. (2002). Evaluation of chapman's neurolymphatic reflexes via applied kinesiology: A case report of low back pain and congenital intestinal abnormality. Journal of Manipulative and Physiological Therapeutics, 66-72. doi: 10.1016 / j.jmpt.2003.11.009