Any copy of X-Plane purchased from X-Plane.com can have the features required for FAA certification unlocked using a special USB key. However, getting the actual certification through the FAA takes a great deal more work than getting the X-Plane software ready.
Certification requires not only that the user have the certified X-Plane software, but also certified hardware (cockpit and flight controls) available through companies like Precision Flight Controls and Fidelity. This is because flight training systems can only be certified as a complete package (a software and hardware combination). The certified software is available for $500 to $1,000 per copy from PFC and Fidelity and the hardware runs from $5,000 to $500,000. The retail version of X-Plane purchased at X-Plane.com is not certified for flight training right out of the box, since certification requires a software and hardware combination. However, the software available for about $80 at X-Plane.com is almost identical what is found in the $500,000 full-motion FAA-certified platforms. The biggest difference is that the FAA-certified versions have custom aircraft files with larger instrument panels, which are set up to work with hardware radios like those found in the physical cockpits. The FAA-certified version also has some of the purely fun stuff (like space flight) removed–even though those situations are simulated accurately in X-Plane, just like the FAA-certified subsonic terrestrial flight.
There is nothing stopping users from getting in touch with the FAA and working through the steps to certification from there. However, most users will find that it is more efficient to purchase a simulator already certified by Fidelity or PFC.
X-Plane.org conducted a quick interview a year or so ago with Mike Altman, president of PFC. For a quick overview of PFC’s certified simulator and the design behind them, read the interview here.