For an ideal tune, it should be done on a Dyno, the best choice being a Mustang Dyno since it simulates actual driving conditions. It takes into consideration the vehicles weight, and loads the drum according to that weight. That coupled with SCT's X Calibrator 2 will give you the ultimate tune. Once tuned, the X Cal 2(handheld) now gives you the ability to manipulate the tune by +/- 2%. It also has Datalogging capabilities. On the Dyno you can also look at AFR, EGT's etc (if Supercharged you can look at boost pressure, inlet temperatures etc). With other software (sneecer) you can look at MAF voltage, injector duty cycles, injector pulse width, commanded advance and a lot more.
Most mail order tunes are based on information provided by the end user, and are 95% on then "rich" side when it comes to fuel, so optimum performance is never gained.
Hope that helps a bit,
Ron