I have a 2006 GT and want to do some cool modifications.  What are best options for more speed and better handling?  What would you do?  

There are a bunch of mods you can do for the 05+. My suggestion would be to visit www.2005stang.com - it's a great site for 05+ mustangs. Lots of great people and a lot of great information on every mod there is for the stang.

Here is what I have done to my 05 GT:
Airaid CAI
Midwest Auto Gear Plenum cover
CDC Hood Struts
Quarter window louvers
Silver Horse Racing deck lid trim panel
SLP Loudmouth exhaust
18x9 Hot Wheels Sixty-Eight wheels in chrome
255/45/18 BF Goodrich G-force KDW NT

Future Plan:
BBK throttle body 62mm
Handling Pak from Ford Racing
Diablo tuner  

Your best gains are going to come from a cold air intake and gears.  Forget the aftermarket throttle bodies....no appreciable gains over the stocker.  Especially for the price.  Stick with a reputable Cold Air intake kit.  FRPP, Steeda, C&L, WMS, AirRaid are all good units.  With the handheld tuner that comes with these units you should be able to knock 4 tenths off your quarter mile times.  Next up....gears.  3.73 or 4.10 will really amplify the "pucker factor" and push you pretty close to the twelve second range.  I'd also go with lower control arms from Steeda, BMR, or Metco.

One other thing...the FRPP Handling Pack is *** good for the money.  

Depends, how much you are trying to spend?  

I would first start out with letting this pony breath. exhaust and a K&N will give you around 10 dollars per horse power. this is easy and affordable.  

If you are serious about performance and willing spend some money, I would advise a Vortech V-2 SQ S-Trim supercharger. I bought it on a whim after seeing it the "79-07 Ultimate Mustang Parts Buyers' Guide" in the July 07 edition of Mustang Monthly. I got 520 hp and 485 lb-ft of torque at 14-psi boost. It's an excellent performance add-on.  

There are a lot of mods for these cars for decent money. My 2006 mustang gt, with just a magnaflow exhaust dynoed at 261.8hp at the rear wheels. A BBK exhaust will get you 10-15 hp, for about $300.00. Of course if you want to spend about 5,000 you can get the vortech hi-out put supercharger, which comes with a air to water after cooler. Just remember the motor is also gonna need some work. A really good comp cam is gonna cost about $700 and, and the most important thing to replace if your gonna get some real high horse power is replacing the connecting rods and pistons $2000...  These are really good motors good up to about 550-600hp with out replacing the rods. and with those little mods getting dyno and tuned, probably somewhere between 600 and 750. dependent on how you tune the car.  

I just recently bought a 2006 V6 Mustang Delux with the premium package.It has all the bells and whistles except for the interior isn't leather, It has the 17 inch wheels with the pirelli tires,the traction control,the shaker 500 stereo, the power seat, every option that you can get for the V6 model except for the leather seats. From what I was told at the dealer ship it's the only one around in South Carolina,Georgia,North Carolina,Tennesee,Florida with the package that it has But I think they are full of you know what. I was looking into the CS6 Package for in the future But heard that the there were some issues since the Trans clutch and rearend couldn't handle the power the motor puts out, 350 Horses. It includes the 20 inch wheels,the larger caliper brakes,the Paxton super charger,the 3.55 gears,the hood,and so on. But from what I understand you need a different trans,clutch, and rearend when you add the CS6 Package. I got the V6 model because of the gas issue.  

Drop as much weight off the car as possible. Weight kills performance!