The Best is pretty subjective. There are arguments by each company as to why they are the best. It really depends on what you are looking for.
You can take a stock GT and grab a $5,600.00 roush blower package (complete with exhaust improvements). Compare that to the 50K price tag of a roush, and then consider the other 12k for the body kits. Status alone, Shelby has the name, and I would consider it The Best imho. Entry Level performance packages seem to be Roush's style, where Saleen tends to be the power house but looses the genuine character of the stang by some pretty awful body kits. But again, you're paying for the image you want.
Heck, the performance of my 05 V6 is better than the older GTs, and for a daily driver the car suits me fine. I can bolt on a Roush blower kit and in a weekend put out 350hp before any major tune to the injectors or computer, if I wanted that. There's so much to work with here, these cars Beg to be built to the individual.
The best thing I have learned is that you cannot buy "off the shelf" the best package and really ever appreciate it. If you want Status, bring money, if you want the Best Package, you build and tune the car to your reflexes, your style, your abilities, it really matters if you are building the car to enjoy or impress someone else.