Apollo Energy Independence Act of 2008

Apollo Energy Independence Act of 2008 - Amends the Internal Revenue Code to provide tax incentives for energy conservation and production, including provisions to: (1) make permanent the tax credit for producing electricity from renewable resources and to include marine and hydrokinetic renewable energy as a resource for purposes of such credit; (2) make permanent the energy tax credit for solar energy, fuel cell, and microturbine property; (3) allow a new energy tax credit for combined heat and power system property; (4) provide for the issuance of new clean renewable energy bonds; (5) increase the tax credit for advanced nuclear power production; (6) make permanent the tax credits for residential energy efficient property, energy efficiency existing homes, the production of energy efficient household appliances, and the tax deduction for energy efficient commercial buildings; (7) allow tax credits for new alternative motor vehicles, including qualified plug-in electric drive motor vehicles, vehicles that achieve a fuel economy standard of 100 miles per gallon, and advanced technology motor vehicles; (8) allow tax credits for the production of cellulosic biofuel and for hydrogen infrastructure costs; (9) increase and make permanent the tax credit for alternative fuel vehicle refueling property expenditures; and (10) allow employers a tax credit for providing transit passes to employees.

Amends the Energy Policy Act of 2005 to provide full loan guarantees for the construction of advanced nuclear energy facilities.

Establishes in the Treasury the Petroleum Reduction Trust Fund. Allocates 90% of civil penalties for automobile fuel economy violations to such Fund for retail purchases of ethanol, biodiesel, and other alternative fuels.

Directs the Secretary of Energy to: (1) carry out research programs for onboard storage of hydrogen in light-duty motor vehicles and for the development of plug-in electric drive vehicle technology; and (2) study daily and seasonal energy costs in public schools.

Amends the Harmonized Tariff Schedule of the United States to extend the tariff duty on ethanol until December 31, 2010.

Directs the Administrator of the Environmental Protection Agency (EPA) to establish a grant program for green school construction and improvement.

Sets forth revenue offset provisions, including: (1) a moratorium on earmarks in the 110th Congress; (2) establishment of fees for oil and gas leases in the Gulf of Mexico and user fees for certain food safety and inspection services; (3) a reduction in payments under the Department of Agriculture commodity program; (4) consolidation of Department of Defense exchange stores system; and (5) a limitation of universal service fund support.