There are two things to insist on when getting a fuel management system for the bike: (1) the hardware and software have to be proven and able to adjust all the operating parameters; (2) more importantly, the person operating the fuel mgmt system has to really know what he's doing. If you get both of these, you'll probably get a good result: bike starts easily, idles smoothly, good drivability, pulls strongly, gets decent fuel mileage, doesn't carbon-up the cylinders, and doesn't run any hotter than necessary.
Some of the full-function "ECM flash boxes" out there are the TTS Mastertune, PowerVision, Screamin' Eagle Tuner, and so on. These actually allow the dyno operator to build a new fuel map and adjust timing, etc. These have the most flexibility and capability--but you need a good operator to do it right. These are generally more expensive, and many must have a full dyno tune (more $$) to get it right, although some companies (like Fullsac with the TTS) have pre-developed maps they provide free when you buy the box from them. Fuel-Moto provides maps when you buy the PowerVision.
Then there are the "piggyback" boxes that don't insert a new fuel map; they just add or subtract fuel at different operating conditions. These are generally cheaper, but they don't have the full adjustment capability of those above. Examples are the Power Commander 5, the Vance and Hines FuelPack, and the "Xied." Oh, and HD has "Screamin' Eagle downloads, which are minimal adjustments to the stock operating system, and are not well respected around here. Also, most (but not all) of the HD dealers do not have a good operator in house, and they mostly just load a canned map that is "closest" to what modifications you've made to the bike. There are a few dealers who have a good guy there, but you need a specific person (see below for more on this).
There's also the ThunderMax, which completely replaces the ECM (Engine Control Module) on your bike. It's expensive, but with the AutoTune capability, it's not supposed to need a dyno tune. Some controversy about it.
So which is best? Much discussion on here about them, and many opinions as well. People have both good and bad experiences with different boxes and operators. The most general advice is "Find a good tuner (the operator) and use whichever box he likes best for your build."
So if you'll tell us where you are and what kind of riding you do, we can give you some specific advice. There are several good dyno tuners known to the members of this forum, and we can steer you in the right direction.