The Stage 1 Flash raises the Rev Limit from 5,800 RPM to 6,200 RPM plus advances the ignition curve and adds fuel. With some pipes the Flash is all you need. In some cases, you will need more fuel, that's where the fuelers (DFO, TFI and SE Race Fueler) come in.
These devices also have their disadvantages. In some cases, reduced mileage because they are fuel adders. They are also one more device to fail. They are not capable of affecting the de-cel enleanment tables which means you can still have popping and back firing.
The next step up (in $ and capabilities) is the SERT or PCIII.
I have two problems with the PCIII; first it does not raise the Rev Limit (they have been promising to correct that since May of '04). Second, it is a separate unit that is added to the output of the stock ECM. If it fails, you are back to a stock tuned ECM.
This is why I recommend the SERT; it has all the capabilities of all of the above, from Stage 1 flashes to custom mapping. It does this by reprogramming your bikes ECM. Plus it has more, such as data logging which can be used to find problems and show you where to make changes to your maps.
You do have the next option which requires more $$. That is a Closed Loop Tuner such as the Daytona Twin Tech. It has the same capabilities as the SERT but does all the tuning automatically. It is not my area of expertise but there are a few here on the forums that use it.
This is my standard answer to any and all EFI calibration hardware questions.