A tune is the "program" that a Programer, like Superchips, Diablochips, and Sniper Tuning, flashes into ECU.
If you want a recommendation, I'd recommend Sniper Tuning since it lets you to customize your own tune. It lets you "upgrade" your tune with your car. For example, you could get it now and make a tune. Then when you do get a supercharger, you can make another tune to accomodate for that.
Just talk to Green03 if you want a custom tune. In my case, shifting was greatly improved.