National Defense Enhancement and National Guard Empowerment Act of 2006

National Defense Enhancement and National Guard Empowerment Act of 2006 - Expands the: (1) authority of the Chief of the National Guard Bureau (Bureau) to include membership on the Joint Chiefs of Staff (JCS) (and raises the grade of the Chief from lieutenant general to general); and (2) functions of the Bureau to include facilitating and coordinating, with other federal agencies and the states, the use of Guard personnel and resources for, and in, contingency operations, military operations other than war, natural disasters, and support of civil authorities.

Directs the Chief to: (1) identify gaps between federal and state capabilities to prepare for and respond to emergencies; and (2) make recommendations to the Secretary of Defense on Guard programs and activities to address such gaps.

Requires annual Department of Defense (DOD) budget justification documents to include separate amounts for Guard training and equipment for military assistance to civil authorities and other domestic operations.

Establishes within the JCS an Assistant to the Chairman of the Joint Chiefs of Staff for Reserve Matters.

Expresses the sense of Congress calling for consideration of eligible reserve officers for promotion to the grades of lieutenant general or vice admiral on the active duty list.

Requires the position of Deputy Commander of the U.S. Northern Command to be filled by a qualified Guard officer eligible for promotion to the grade of lieutenant general.