Thought I'd start a new topic/discussion with it's own heading to make it more find-able.
Now I happen to have a little time under my belt, mapping ECU's (about 7 years worth). So for what it's worth, here's a brain dump.
Feel free to add to / correct / dispute / comment.
It is a very technical issue we are dealing with.

And it depends on your required mixture (pun intended) of outcomes

Drive-ability improvements, power improvements, fuel economy, and of course the ones that manufacturers are legally obliged to confirm too, emissions.
Assuming the lean mixture is the only problem... which is almost never the case, but a slightly richer mixture CAN improve smoothness / affect fuel consumption (up or down).
Note of warning: Most folks add stuff when a tune-up is required, then go ahead and test the bike.
The benefits of a tune-up PLUS an add-on are going to make the owner feel much better about the add-on accessory. Therefore speak highly of the add-on.
The cost of doing a pre-tune-up dyno run PLUS a post-tune-up dyno run PLUS a post add-on run are usually not what people are prepared to splash CASH for.
Some scenario's... (Not exhaustive, but wide enough for this discussion)
. 1. Air/Fuel Ratio Control - Tricking the ECU by making the mixture richer only (Power Booster plug, and many variations) (with all sorts of variations of speed / load / rpm settings).
Simply adds an offset to the signal sent from the oxygen sensor in the exhaust which basically tells the ECU that the engine is colder than it is.
Cheapest solution and assumes that the device will automatically adapt to adding other engine goodies
Small and easy to hide, dependent on the product.
Can be removed from bike to return to standard and maybe re-using on the next bike, assuming it fits.
2. Air/Fuel Ratio Control - Plugging in aftermarket boxes after between the ECU / Injectors / Fuel system (Wunderlich/Interceptor)
More complicated, in that it has a set of external maps that adjusts the fuel injector output post ECU signal.
Don't know how it gets around the oxygen sensor then telling the ECU that it is rich according to the stock map inside the ECU.
Cheaper solution and assumes that the device will automatically adapt to adding other engine goodies
Packaging size can be an issue, dependent on the product, may require some space and wiring to fit.
Can be removed from bike to return to standard and maybe re-using on the next bike, assuming it fits.
3. Ignition and A/F Ratio Control - Plugging in aftermarket boxes after between the ECU / ignition / Injectors (Power Commander III, etc)
Not cheap but a better solution. Most of these manufacturers have a large listing of maps (for individual bikes) which are updated by manufacturer and user experience.
More complicated, in that it has a set of external maps that adjusts the fuel injector output AND ignition parameters post ECU signal.
Often is packaged with their own oxygen sensors.
This type of product acknowledges that there a more parameters to engine mapping than simple air/fuel ratio.
Maps are usually available on their websites for downloading if other engine goodies / exhausts / cat removals / air filters are added later.
Packaging size can be an issue, dependent on the product, may require some space and wiring to fit.
Can be removed from bike to return to standard and maybe re-using on the next bike, assuming it fits..
4. Re-mapping the ECU with a new map that modifies all parameters that control the operation of the engine / combustion / ignition / Injectors (BB Power, Hilltop Motorcycles, etc)
Best solution (if done well with proven technical experience, extensive/expensive dyno time)
Not complicated but completely technical as all ECU parameters are modified.
This can reap smoothness, unleash power, improve fuel consumption (dependent on the amount of extra power one chooses to use, of course).
Zero packaging issues as no extra boxes or wiring are required.
Whether it is adaptable to add-ons is not known, but MOST engine ECUs seem to be to cope with adding an exhaust can and filter which is all most people do. BMW for example do allow an Akro system without modification to ECE.
ECU needs to be removed/fitted and shipped to the place of modification and back. (Most people want it now).
Non-transferable back to standard or to another bike unless it is the same. But the new owner will be very happy


No simple solutions really.
Use your dollars wisely

Websites for products discussed:
BBPower Germany: http://www.bbp.homepage.t-online.de/r1200gse.htm
Wunderlich Germany: http://www.wunderlich-bmw.com/en/shop/20/tuning/3/
Booster Plug: http://www.boosterplug.com/shop/bmw-r12 ... -15c1.html
Power Commander: http://www.powercommander.com/powercomm ... 0III%20USB
Hilltop Motorcycles: http://www.hilltopmotorcycles.com/
Hilltop Motorcycles Interceptor: http://www.hilltopmotorcycles.com/shop/ ... goryID=149
Interceptor: http://www.bikeinterceptor.com/products ... nterceptor