Medicare Prescription Drug Affordability Act of 2008 - Amends part D (Voluntary Prescription Drug Benefit Program) of title XVIII (Medicare) of the Social Security Act to: (1) limit Medicare part D prescription drug plan (PDP) cost increases to the Social Security cost-of-living increase; and (2) direct the Secretary of Health and Human Services to negotiate with pharmaceutical manufacturers the prices that may be charged to PDP sponsors and MedicareAdvantage (MA) organizations for covered part D drugs for part D eligible individuals who are enrolled under a PDP or under an MA-Prescription Drug (MA-PD) plan.