Plug-In Hybrid Electric Vehicle Act of 2006 - Directs the Secretary of Energy to: (1) conduct a program of research, development, demonstration, and commercial application of technologies needed for the development of plug-in hybrid electric vehicles; and (2) establish a competitive grant pilot demonstration program to provide up to 25 grants annually to state and local governments and metropolitan transportation authorities, or combinations of them, to implement demonstration projects for plug-in hybrid electric vehicles.