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I have an 05 f150 with the 5.4l, and recently purchased the Sniper Commando and Special forces software, I love it. It made a huge difference with my truck, now I can change my tune at any time and try different settings. I also tuned my mother in laws 4.6l f150 wow! what a difference. I would recommend them. Lastly there customer support is top notch.
I've been using SCT/PRP on my GEN 1 Lightning and 94 F-150 for roughly 5 years now and it works great. One added benefit with OBD-2 is datalogging; you can download and install Live Link and datalog through the Xcal, to your laptop, and I believe LL is included with the purchase of your tuning software.
SCT's package is top-notch, easy to use and tons of features, plus its supported and development is active.
HP Tuners also makes a good package. User interface is a bit easier to use than SCT's for the beginner, but requires more menus, mouse clicks, etc. for someone after they get familiar with tuning.
The tuners are independent hand held computers. They can connect to standard Windows PCs via a USB port to update the software on them, handle data logging, etc. They cannot cannot to Windows Mobile PDAs.
I've been using the SCT Pro-Racer software for about 5 years. It's not cheap and not to be insulting, but unless you very familiar with the parameters and strategies that go into the PCM, you might be better off working with a tuner and telling him your mods and working with him to get your tune.