Great thread!
I use the SE Race Tuner. I chose that unit for the wide range of adjustment that it provides. I am riding a '08 Ultra with a SE Air Cleaner and SE slip-ons, modest improvement in performance, but with the SERT I can get the most performance for the setup. I don't remember what I paid for the SERT, but seems like it was over $500 with the cables.
I also make use of a "poor man's dyno" a G-Tech Performance Computer and a Innovations Fuel-Air meter. These two tools are critical to get the most out of a tune. You program the Performance Computer with the weight of the bike and rider and it will print out a horsepower curve from an accleration test. It also can record your 0-60 and 1/4 mile times. Very handy for gauging your progress as you tune. It takes more time to make the runs compared to running the bike on a dyno, but the unit itself costs less than one typical Dyno session at the dealer.
The SERT comes with a number of MAPS. I start with a map that is close to the modifications on my bike, hook up the F/A meter and the Performance Computer and take some data points. One of the things I like about the SERT is its ability to be used as a data acquisition system while you ride the bike. Set it up to acquire data with your laptop, push the red button to start data collection and ride the bike. When you are done you can download the data and display it on your computer. Just about every parameter of the fuel computer is available for display, ignition timing, O2 voltage, RPM, CHT, vehicle speed, integerated O2 sensor voltage, injector pulse width, and on and on!
The SERT allows you to adjust just about every parameter of the EFI. You can view the maps in table or graph mode. You can save different revisions of your maps as you develop them so you can always go back if you have too. You can also save notes in the map files.
I am not done with tuning the '08 but it is much better than stock. I've gained 9 miles per gallon in highway crusing and trimmed almost a full second off the 0-60 time on the bike. The bike runs great, runs cooler and is quicker. Hard to beat. The SERT is not the cheapest way to go, but it is the most complete solution I have seen.