Factory to factory the SVT Cobra is faster. Both have 4.6 V8s , just a cobra is 32 valve vs. 16 in a GT. Cobra is supercharged and GT is not. Cobra has a lot more suspension difference that makes it faster all around.
03 and 04 were the only ones supercharged from factory as Truth says above
SVT Cobra is much faster. Also, the Cobra is NOT just a GT with a supercharger, the cobras are completely different. The Cobra has a 4 valve per cylinder V8 engine that is hand build by 2 guys and comes with a cast iron block and all forged internals. The GT comes with a 2 valve per cylinder engine with an aluminum block and no forged internal components and the engine is made on an assembly line by machines. The cobra engine because of the forged internal components, crank shaft, and cast iron block can handle up to and over 1000rwhp. Since the GT has an aluminum block and no forged internal components it can only handle around 500rwhp at very best. The cobra comes with a tremec T56 6 speed transmission which is one of the strongest and best trannys you can get and can handle up to and over 1000rwhp, it is the same tranny that comes in the $80,0000 dodge viper. The GT mustang comes with a basic 5 speed tranny that can not handle more then 500rwhp. The cobra comes with heavy duty racing brakes, the GT has just normal brakes. The cobra comes with an independant rear suspension, the GT comes with a solid suspension. The cobra has 17x9 inch rims, the gt has 16x8 so you can put 315's on the cobras where the widest tire you can put on the GT is around 255's. I could keep going on but I think you get the idea. The 03/04 cobras (nicknamed "the terminators" because of there ability to terminate the competition) are the fastest cars you can get for the money. They can run 12.8 and 12.9 quarter miles with the most novice driver. Evan Smith from Fast Fords and Muscle Mustangs ran a 12.43 with a completely stock 03 cobra. The fastest GT runs a 13.7 quarter mile at best.
SVT is the fastest production you can get from ford (not considering saleen, roush, yada yada), the cobra makes the highest hp and tq and as far as model year the 03 and04 i believe comes supercharged from the factory and has the highest hp and tq rating out of the year range and has the fastest 1/4 mile to my knowledge
also the 03 and 04 svt models were the only ones to be supercharged from the factory. the guy above me datwikracer is incorrect