After looking over the different programmers available for a 99 GT, I really dont see any major differences between them. Has anyone found one to be easier, more beneficial, or anything else? I just got the car and it is a completely stock 5 speed convertible all the way down to it's 16" wheels. From what I have gathered, having the programmer will help with any other mods later, correct?  

Definitely get a programmer for that car. SCT seems pretty popular, but honestly, I'd just go to whichever Mustang shop is closest to you and ask which one THEY like to tune with. Unless you're dealing with a mail order tune (which is fairly common) you'll end up in the local shop for retunes whenever you make significant mods. (like forced induction) It's good to establish a relationship with a local tuner now so you're ahead of the game later.