I agree with the above comments about the GT takeoff mufflers. They give you about the same performance of any hi-po aftermarket single or dual system, are calm at cruising speed and howl at wide open throttle. Stay away from flowmaster, magnaflow, borla and most other hi-po systems unless you want LOUD, because thats what you're going to get with most of them.
A cold air intake and custom tune will get you the most horsepower and torque increase, but they cost from $450-600+ depending on the brand. Tunableinduction.com has a great kit and it costs like $480 with a tuner.
Your next step after that should probably be gears and a limited slip differential. This will help you put your power to both rear wheels instead of just one.
Other smaller mods to consider are underdrive pulleys, a screamin' demon coil pack (with livewires), a 4" aluminum drive shaft and a short throw shifter (manual only).
Stay away from JET chips or any kind of chip that plugs into your car. Get a tuner like diablo predator or SCT's X-calibrator. Also stay away from throttle body spacers as they cost over $200 and yield absolutely no performance gains. Aftermarket headers don't do much for the 4.0 either, so they're really more of a preference mod than anything.
__________________
Black 2005 Mustang v6, 5 speed, IUP, EUP and Leather.
Razzi 1/4 window scoops, Mustang GT Sway Bars, Flowmaster American Thunder Single Exhaust, Clear Front Turn Signal Lenses, Demolet CAI, X-cal2 91 tune, Hurst Comp/Plus Shifter, FRPP T-Lock, Ford 3.73 gears