Yes, apartment buildings and other multi-family housing (more than 3 stories) are eligible for the commercial building tax deduction. The relevant standard is the one cited in the statute ASHRAE 90.1-2001. Learn more about tax deductions for commercial buildings.
NOTE: In December 2015, Congress passed legislation that reinstated the deduction for 2015 and through December 31 2016. The legislation also modified the referenced ASHRAE standard. For projects placed in service after December 31, 2015, the 2001 edition of the ASHRAE standard has been replaced with the 2007 edition.