Empowerment Zone, Renewal Community and Enterprise Community Enhancement Act of 2009 - Amends Internal Revenue Code provisions relating to tax-preferred empowerment zones, rural enterprise communities, and renewal communities to: (1) extend the period of designation for such areas through 2015; (2) provide a safe harbor standard for employee residency requirements in empowerment zones; (3) eliminate certain residency requirements for the empowerment zone employment tax credit; (4) grant authority to expand the boundaries of empowerment zones and enterprise communities, including those located in rural areas; (5) allow carryovers of unused expensing allowances for enterprise zone businesses; (6) allow certain empowerment zone businesses to elect to receive payments in lieu of tax benefits; (7) allow federal guarantees and tax exemptions for enterprise zones and renewal communities; and (8) allow the issuance of tax-exempt rural enterprise community bonds and empowerment zone facility bonds.