Empowerment Zone and Renewal Community Enhancement Act of 2006 - Amends Internal Revenue Code provisions relating to tax-preferred empowerment zones, enterprise communities, and renewal communities to: (1) extend the period of designation for empowerment zones and renewal communities 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, enterprise communities, and renewal communities (requires expansion of such communities located in rural areas upon the request of a local government if specified conditions exist); (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; and (7) allow federal guarantees and tax exemptions for enterprise zone facility bonds.