I couldn't say which is best but the first mod I made to my 05 V6 was a JLT CAI with an SCT performance tune and wow what a difference. If you are going to install a CAI please install a tune as well!
I put a C&L CAI, Bama Tuner and Flowmaster Force II Cat-Back on mine and it made a huge difference. I went with the Force II (3 Chamber Mufflers) to keep it legal for Germany, which is a maximum of 95 dB, where mine is running at 93.2 dB. All this is around $1200, give or take depending on where you buy it and what deals you can get. Currently I have NGK Iridium Spark Plugs, Taylor plug wires and a Screamin' Demon Coil pack on the way, and eventually I'm going to get a new driveshaft, Corbeau seats, 5 point harnesses and rear seat delete. And for suspension, American Muscle has an Eibach Pro-Sport Suspension kit, which includes shocks/struts, and sway bars for around $900.
That being said, it all depends on what you want out of your V6. If you want to increase the top end speed, you MUST, I repeat, MUST replace the driveshaft because the stock shaft will explode at around 130 mph. If you want better acceleration you can get some rear end gears and a limited slip. If you want overall power you could always go with a supercharger or turbo, though that will cost quite a bit. You can get forged internals and port and polished intake from Super Six Motorsports. Just look around, it all depends on your price range.