Now that 2007-2011 ACS 5 year data is available in the API, please see this guidance on comparing ACS data.
From the page:
The Census Bureau recommends that you:
DO compare estimates from non-overlapping periods, for example, compare a 2005-2007 ACS 3-year estimate to a 2008-2010 ACS 3-year estimate.
DON'T compare overlapping periods, for example, the 2005-2007 ACS 3-year estimates to the 2006-2008 ACS 3-year estimates.