IMO, you can't go wrong with any of the performance upgrade options out there. They will almost all give you what they claim they will. The exceptions to that IMO are the claims by some of the vendors (Banks and Dr. Performance come to mind directly) that using their products will not void any part of your warranty. Here's a couple of posts where there were extended warranty discussion:
Banks and
Dr.Performance. Another major exception is Dr. Performance's claim that they do not add fuel or air or raise your EGT's. That's a physical impossibility - it's called a perpetual motion machine. Dr. P does add power to your truck but they will also raise the EGT's. Was talking to a vendor just this weekend that had a guy with one of Dr. P's kits on his truck and he asked the guy what his EGT's were - he said he didn't know because he didn't need gauges. After discussing it with him for a while the guy bought a set of gauges off of him. After he installed them he told the vendor something was screwed up with his EGT gauge because it was pegging at 1500 degrees

! They went out and popped the hood on his truck and after seeing the exhaust manifold told him he's been running that hot for a long time - nothing wrong with the gauge!
I've had a major fueling box on my truck for 65,000 miles now (TST Powermax - have had several different programs on it) and this last weekend at Scheids TST had their engine simulator and an oscope there. In talking with Mark about how it works, the limits, what you can change, etc I decided to have mine programmed with a custom program (noone else has the same program that's in my box now). I love how my truck is running now (loved it before too, but more now)! I also added his EGT and boost gauge module to the box so it has automatic defueling that I can set. It was awesome towing my trailer home and having the EGT limit set at 1200 degrees. I was able to run on level 7 and get the immediate rush of power for passing, etc - but on a long pull it would automatically defuel to stay at 1200 degrees.
Now having said that, now that I understand much better how the major fueling boxes work IMO there isn't much if any difference between the current major fueling boxes. As long as they plug into the MAP sensor and the fuel box wire (some early boxes didn't plug into the MAP sensor) then they COULD all be the same if they put the same parameters into them. They can set an overfueling amount based on RPM and boost (max of 50% on the Powermax3 street version and 90% on the Powermax3 comp version), they can adjust the curve of that addition so it hits harder on the bottom end or the top end, they can also set a max solenoid duty cycle (when the solenoid is open fuel is flowing to a cylinder - the same solenoid send fuel to all the cylinders in a VP44 so the absolute max you could have is 99. 9% duty cycle because it needs to close to move onto the next cylinder). The higher you go on that duty cycle the hotter the solenoid will get (and possibly melt) and more length of the slot in the rotor will be used. What you have to decide is how high you want to go. The hotter the box the more heat you are putting into that solenoid. What I'm trying to say here is all the boxes work on the same principles, it's what program is put into the box. My recommendation would be to go with the manufacturer that's closest to you or that you feel comfortable with their customer service. In my case TST is about a 6 hour drive and they've bent over backwards to make me happy. They do make it VERY clear to you that you are taking a chance with your warranty. For an interesting take on why the VP44's fail check out this paper written by Chip of Blue Chip Diesel:
VP44 pump failures explained.