First, choose the company/tuner you want to provide you with custom tunes, then use the handheld flash tuner they recommend.
I used to use the Predator from DiabloSport. But when I switched from Sal at PSP to JJ at Woodbine Motorsports for my tuning needs, JJ didn't use the DiabloSport software, he uses SCT. So I had to switch to a SCT handheld, and opted for the Xcal 2.
Lotta guys are liking the Sniper tuning software too.