Hudson-Fulton-Champlain Quadricentennial Commemoration Act of 2006 - Directs the Secretary of the Interior to establish: (1) the Champlain Quadricentennial Commemoration Commission to plan and execute programs and activities to commemorate the 400th anniversary of the voyage of Samuel de Champlain (the first European to discover and explore Lake Champlain); and (2) the Hudson-Fulton 400th Commemoration Commission to plan and execute programs and activities to commemorate the 400th anniversary of the voyage of Henry Hudson (the first European to sail up the Hudson River) and the 200th anniversary of the voyage of Robert Fulton (the first person to use steam navigation on a commercial basis).