those are programmable reprogrammable engine management systems to give the rite amount of fuel at the rite time to create the best air fuel ratio = more power ems is by aem both are good hondata cost more and would be my choice simply cause honda makes it.plus check the last issue of scc they have a whole story on the hondata and what its suposed to do.
Hondata modifies standard OBD I Honda ECUs, adding features and expanding the capabilities of the ECU (to read boost for example). For best results naturally aspirated ECUs should be tuned to each individual engine setup and forced induction ECUs must be tuned (by a dealer or with ROM Editor). If you have Stage 4 and the Pocket Programmer, you can tune stages 2 and 3 for others.
AEM E.M.S. Engine Management System:
AEM's Plug & Play Engine Management System (EMS) is the first of its kind and will forever change the way you look at fuel injection tuning! This user-programmable system plugs directly into a vehicle's factory ECU harness and requires no additional wiring. Windows™-based software (2000, NT, 98, 95, ME) makes the task of copying, viewing and manipulating data as simple as a click of the mouse. User-defined templates are easily configurable and enable tuners to establish "quick keys" to any pertinent information during the tuning process. The AEM EMS's infinitely-adjustable software allows tuners to program virtually any combination of engine control, power adders and auxiliary devices, and accurately deliver proper amounts of fuel and correct ignition timing for ANY boost level or operating condition.
If you are going to have someone tune the car for you, get the Hondata. It's much cheaper to just get a Hondata Stage 2 even after adding in the OBD2-1 conversion. Use the extra money for some good dyno tuning sessions with the Hondata tuner in your area. And no, Honda is not affiliated with Hondata whatsoever.
If you actually know what you are doing and are going to tune the car yourself the AEM EMS may be a better investment. You plug it in and go and it's much easier to work with than Hondata. The cost of a Hondata Stage 4, OBD2-1 conversion, plus burner would be equal or more than what you'd pay for an easy plug and play AEM EMS.
Since you don't know enough to tune everything yourself I'd say go with the Hondata Stage 2 and have a shop tune it for you. Your area and car aren't specified in your profile so I don't know if you'll need OBD2-1 conversion and don't know what shop in your area would be good with Hondata tuning.
The Stage 4 will allow you to tune maps yourself like the AEM EMS will but you may still need an OBD2-1 conversion with it which is why the AEM EMS would be a better choice if you were to do the tuning yourself.
I have the EMS, but I'm scared to tune it myself since the system is just soo new and it hasn't been around yet. I'll probably end up having someone tune it for me.
Like SurferX said, you might want to go the Hondata route for simplicity reasons. The EMS is more advance that you don't have to burn new ROM for every new map that you want. All you do is load it up and run it.