H-Prize Act of 2006 - Directs the Secretary of Energy to award competitive cash prizes biennially to advance the research, development, demonstration, and commercial application of hydrogen energy technologies.

Instructs the Secretary to encourage broad participation, including by individuals, universities (including minority-serving institutions), and large and small businesses (including those owned or controlled by socially and economically disadvantaged persons).

Directs the Secretary enter into an agreement with a private, nonprofit entity to administer the prize competitions.

States that funding sources for such cash prizes shall consist of federal appropriated funds and funds provided by the administering entity.

Designates prize-eligible categories, including: (1) advancements in certain hydrogen components or systems; (2) prototypes of hydrogen-powered vehicles or other hydrogen-based products that meet or exceed certain performance criteria; and (3) transformational changes in technologies for hydrogen distribution or production that meet or exceed far-reaching criteria.

Declares that the federal government shall not, by virtue of offering or awarding a prize under this Act, be entitled to any intellectual property rights derived as a consequence of, or direct relation to, the participation by a registered participant in a competition authorized by this Act.