Physician Workforce Enhancement Act of 2009 - Amends the Public Health Service Act to require the Secretary of Health and Human Services, acting through the Administrator of the Health Resources and Services Administration, to establish a loan program that provides loans to eligible hospitals to establish residency training programs. Requires that such program be an allopathic or osteopathic physician residency training program in family medicine, internal medicine, emergency medicine, obstetrics or gynecology, general surgery, preventive medicine, pediatrics, and behavioral and mental health. Requires the Administrator to give preference to hospitals in a rural area or an urban area that is not a large urban area.