Homeowner Empowerment Act of 2008 - Amends the Internal Revenue Code to: (1) exclude from gross income distributions from individual retirement plans and other qualified retirement plans for payments on the mortgage of a taxpayer's principal residence; (2) require repayments of amounts distributed from such retirement plans over a 12-year period; and (3) waive the 10% penalty on premature distributions from retirement plans for distributions used to pay a mortgage.