Saving Energy Through Public Transportation Act of 2008 - Authorizes appropriations for each of FY2008-FY2009 for public transportation formula grants for urbanized areas and for other areas. Authorizes the Secretary of Transportation to make such grants for: (1) operating costs of equipment and facilities being used to provide the public transportation that the grant recipient is no longer able to pay as a result of reducing fares; and (2) operating and capital costs of equipment and facilities being used to provide transportation services that the recipient incurs as a result of expanding such services. Requires the federal share of the costs for such grants to be 100%.

Requires a grant for FY2008-FY2009 that involves acquiring clean fuel or alternative fuel vehicle-related equipment or facilities for the purposes of complying with the Clean Air Act to be for 100% of the net project cost of the equipment or facilities unless the grant recipient requests a lower percentage.

Amends the Safe, Accountable, Flexible, Efficient Transportation Equity Act: A Legacy for Users to require: (1) qualified federal agency employees serving in urbanized areas of the United States that are served by fixed route public transportation to be offered transit pass transportation fringe benefits; and (2) the Secretary to issue guidance on nationwide implementation of a transportation fringe benefit program.

Requires the Secretary to establish a pilot program to carry out vanpool demonstration projects in not more than three urbanized areas and not more than two other areas.

Requires a grant for a capital project during FY2008-FY2009 that involves the acquisition of real property for, or the design, engineering, or construction of, additional parking facilities at an end-of-line fixed guideway station to be for 100% of the net capital cost of the project unless the grant recipient requests a lower percentage.