E-85 Investment Act of 2006 - Amends the Internal Revenue Code to modify the tax credit for alternative fuel vehicle refueling property by: (1) increasing to 75% the rate of such credit for property using 85% ethanol fuel; (2) reducing the maximum dollar amount of such credit in 2013 and 2014 for ethanol-related refueling property; and (3) extending such credit through 2016 for ethanol-related refueling property.