Most guys doing tuning on this forum either use the SCT PRP package or the Binary Editor (BE) system from Popsracing.com .
Both systems work and have their pluses and minuses, the SCT system has broader support as most pro tuners use it so there are more options to8 have a pro work with you on the tune.
The BE system has better datalogging, broader hardware support and some additional features not available with the SCT system.
With the BE system if you already have a pro tune in the car you can read it in and use it as your starting point.
I believe the BE system also lets you access portions of the tune you can't access with the SCT system but I could be wrong about that.
The BE system also allows you to either tune via flashing your EEC, like the SCT system does, or you can use a hardware system called QuarterHorse that actually allows you to make tune adjustments in real time while the motor is running, which is pretty slick.
The BE system isn't perfect but its pretty reliable once you get it set up.
On my 02 GT I could never get data logging to work reliably with my SCT X3, even after many calls to their tech line and multiple reflashes of the SCT unit, it would never datalog reliably.
Unfortunately this is an issue with the SCT devices on our year cars but it seems to be hit or miss, it works fine for some guys but others like me just can never get it to work.
In contrast once I got it settled down the BE system has been pretty reliable.
If you are interested in BE call Adam at popsracing, if you buy the system he'll log in to your PC and get it set up and get you to the point where you can write your first tune.
He's also a well respected tuner and for addition cost will also do remote tuning.
Whichever direction you decide to go, definitely get Don Lasota's book on tuning from: LaSota Racing Ford Tuning & Training
Also the forums and sites below have useful tuning information and you can get help and suggestions from other tuners:
EECTuning.org ? View forum - Tuning the EEC....
EFIDynoTuning ? Index page
EFIDynoTuning / Index