Thats like asking a group of guys what beer to drink. If there are 10 guys, you will get 10 answers. What will the car be used for? Street, track, or strip? For a tune, I prefer SCT by far because they use actual Ford software (its not a hack). The livewire is a great tuner, and offers a lot, but its expensive. If you want to go cheaper, you can get the normal handheld tuner. Either way, you need one for a shop to put tunes on when you get the blower, datalogging, some end user parameter adjustment, and reading/clearing codes. For the exhaust, just look around for a good price. The two Magnaflow threads on here will give you somewhere to start. For an intake, its again personal preference. Find one that looks good, and gives you the power you want. MMR just released theirs, and it has an S&B dual cone filter (good brand). Requires no tune, but they havent released the dyno graphs for it yet.
There are 10 types of people in the world. Those who understand binary, and those who do not.