This may be a base question but what are the functional differences between a stock and an aftermarket ECM? When is it advantageous to use one over the other?
That’s kind of like saying “What’s the difference between an apple and other fruit that is not an apple.” It depends largely on what the aftermarket unit is designed to do. The idea is that the aftermarket ECU will let the car do things that it won’t do stock - for example change the operating parameters to emphasize power output over mileage. From the factory the car may be set up for a good balance between performance and fuel economy, but if you’re planning to get competitive with the car it’s better to emphasize performance and not worry so much about economy.
But you have to be careful because there’s a lot of snakeoil out there. Be especially skeptical of guys who claim their chip will improve both performance and fuel economy, because especially these days, they’re probably full of it - if doing that were possible at a reasonable cost, it’d have been done in the stock ECM.
Where aftermarket ECU/Ms come into their own is when you start modifying other things on the car. If you slap a bunch of parts on that increases air and fuel, and lowers exhaust restrictions, but the stock ECU isn’t capable of adjusting the engine parameters to take advantage of those things, then you’ve wasted your money unless you put a computer in there that can deal with them.
If you’re not modifying other things on your car, it’s almost always pointless to swap out ECUs.
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@shadowfax pretty well sums it up. The only thing that I would add is that some aftermarket ECU/M’s are for off road use only, i.e. racetrack. They will not pass the emissions tests.
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Both @keith and @shadowfax make very good points.
I’ll add one more point; aftermarket ECU’s generally don’t communicate well, or at all, with other systems in the car that really NEED to communicate with the engine ECU. Most notably, the ABS/Stability Control/Traction control computer. Other things, like gauges, also depend on communication from the engine sensors attached to the ECU.
A few years ago, we had a post from a woman who owned a very-new Ford Pickup Truck (F-250? F-350?), and she bought-into the BS that was being spewed by a guy selling ECMs that were “guaranteed to boost power output”. When her engine self-destructed shortly after installing that super-duper ECM, Ford denied her warranty claim–as it should have–and she had to bear the total cost of having a new engine installed.
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It should also be noted that unless you’re doing something really, really, radical. The stock ECU on modern cars can be reprogrammed to do whatever it is you need it to do most of the time. The Ford EEC-V on my old Mustang was able to be reprogrammed (tuned) to run the engine happily even with the addition of an aftermarket supercharger.
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I’d forgotten about that lady. What an expensive lesson.
Yup. But if you’re lucky enough to have something cool and older…
Anyone remember ZDyne? Back in the day we thought that was amazing, being able to plug a laptop into the car and change things around. Of course, those were also the days before GPS and smart phones and wifi-controlable garage door openers. We had no idea how primitive we were. 
For the ordinary car owner there wouldn’t be any advantage to a non-stock ECM. Other than the possibly the stock ECM just is no longer available. Folks who buy aftermarket ECM’s do so for the most part b/c they are attempting to customize their car in some way or another, usually to increase engine power or mpg, or to add some function that wasn’t available for the when purchased new, like electronic fuel injection/electronic ignition, or a turbo-kit/supercharger-kit. i.e. not something a normal owner would ever do with their family car. Their teenager might tho, when the parents are away for the weekend !
You can look at it this way also. The ECM or PCM in your car is basically an aftermarket because the car manufacturer did not produce the ECM/PCM.
Odds are the original factory OEM ECM/PCM comes out of the same factory as the ones sold at various parts houses and online. The stamps and stickers will vary but that’s it.
This is based on stock use ECM/PCMs only.
Thanks everyone!! This has been quite enligtening!
Can one do this on their own? Where is the interface for the unit?
Yes you can to varying degrees. The interface is the OBD 2 port. You can plug in a “programmer” purchased from a variety of sources that comes with a “tune” or calibration set specifically for your car. Additional minor adjustments are usually included as well for you to customize the tune.
Or you can order software and cables for your laptop from a company like HP Tuners that allow you to change every parameter in the ECU. You can tune to your heart’s content but without a rolling road dyno to test your tune, you are working in the dark. The problem with that software is without the proper training on what parameter affects which engine function and how, you can destroy your engine in a heartbeat.
There are experts for nearly every car make that have a rolling road dyno and the knowledge to safely tune your car as it sits now and with any modifications you wish to add.
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