Ford Repair: OBD II 042, obd ii, emission requirements

Question
Can you address the need to reprogram the PCM prior to parts replacement. I understand there are a few TSBs outlining this but have not seen anything that a layman can understand.  

Answer
Jackson, the PCM is the brain that takes sensor inputs and makes the decisions that it sends to the various outputs... you didn't mention any particular application, so I'll stay generic in the function.
The PCM of recent model years has been one that can be 'flashed' or 'reprogrammed'.  This is much easier and less expensive than having to replace it with one that has a later program in it.  Of course, it requires more shop equipment to flash a PCM, and only the dealer will have it due to Federal emission regulation requirements.
Occasionally, the manufacturer will develop a major change in a component, usually as a cure for a concern that a previous release had.  One example I can think of is the ICP (injection control pressure) sensor on the early-built 6.0 Powerstroke diesel.  The later sensor was retrofitted to the early engines, but requires a later program to utilize the new expected readings.
Most times, the PCM update programs do not require any new parts; the program is simply changing the parameters of calculations the PCM makes.  All PCM programs have to be tested by the manufacturer and submitted for EPA approval and certification prior to release.  (That can be months in development and more months in certification)  All of this is to insure that the vehicle will comply with fuel economy and exhaust emission requirements.  
Finally, there are perhaps a few exceptions to the rules above:  Saleen, for example, is another company that can reprogram the PCM for a Mustang that they have modified.  They are a hi-performance company that develops and certifies the cars they modify, and have the EPA certification to make the changes.  There are some aftermarket 'chips' that can be added to various vehicles for change power levels, and they are added to the open slot in the PCM - they should have been certified by the manufacturer of the chip.  However, they are usually not compatible with the original manufacturer's test equipment, so the addition of a chip makes future diagnosis difficult.
Hope this answers your questions.... anything more specific, just write back with the details.
Clay