There's no other tunes for the v6 right now. So it's either get a tune, or don't get a tune. You can't choose SCT or diablo or whatever. Its only Unleashed which uses SCT.
SCT has by far the most support by the tuning community, it data logs, can read & clear DTCs and is all around a solid choice.
Cobb's device has the same ability as the SCT plus the ability to program your ECU so you can change tunes on the fly. You pay a premium for it over the SCT X4.
DiabloSport doesn't have the support in the tuning community that SCT and Cobb have so you are mostly stuck with the canned tunes they provide.
Livernoise is proprietary and has no logging features.
NGAUGE is new to the market and has minimal support plus the company that makes provides no specific platform support but it is a cool device that can be mounted like a gauge.
Your best bet is to choose who you want to get your tune from and use the device they work with.
Here are the benefits that I have personally seen with the SCT X4 with a 91 Octane performance tune from Torrie at Unleashed:
Better throttle response, slightly quicker shifts, bit more power at the top of the rev range. When I ordered the tuner I only had a muffler delete done on my car. I have since gotten an H pipe and have a Roush CAI on the way. When I get the intake I will do a datalog and send it to Torrie and he will revise my tune and I should see more gains.
The cons are that you are voiding your factory warranty with a tune, you may flash back to stock at any time and supposedly Ford won't be able to tell you had a tune, but I'm not sure if that's true or not, I've done some research and found mixed answers. Other than that I've never heard of anyone having any problems with any of Torrie's tunes. His customer service is top notch, send him an email or message here on the forum and you will have a reply in no time, can't say the same for many companies.