As of May 2015, people can use the X-Plane flight simulator to get FAA certification. However, the retail software alone is not sufficient. It's necessary to purchase a custom version of the software and custom hardware to certify the complete package as a flight training system.
The X-Plane software must be combined with specific cockpit and flight controls before using it for FAA certification. Precision Flight Systems and Fidelity sell the required hardware along with the certified version of the X-Plane flight simulation software. The certified software costs about $500 to $1,000, and the hardware costs in the range of $5,000 to $500,000.