Each vendor can create a "custom" tune using the SCT software. They mainly modify such parameters as timing and Air/Fuel ratio to maximize horsepower. The SCT tuner is just a tool for creating a "custom" tune. Check out the Mod forums for more details.
Some tuners may be more conservative (safer) on their tunes than others. Some tunes will require higher octane fuel due to the timing curves that are programed in.....Due your research before you select one.