Just thought I'd share the results of my recent day on the dyno over at MAC Autosport in Parker, CO. See charts below:
Baseline Run: 3/18/09 - Factory intake, JBA headers, TRD Exhaust -
293 RWHP; 324 RWFTLBS (Corrected)
Baseline Run Before Tune: 5/15/09 - TRD Supercharger, JBA headers, TRD Exhaust, URD MAF Calibrator (empty map) -
441 RWHP; 469 RWFTLBS (Corrected)
Final Tune: 5/15/09 - TRD Supercharger, JBA headers, TRD Exhaust, URD MAF Calibrator (tuned map - 10.5-11:1 AFR) -
466 RWHP; 501 RWFTLBS (Corrected). With 20% Driveline loss this is 583 HP/627 ft-lbs at the crank (Corrected of course)
That's right folks - The TRD supercharger with tune netted me 173 HP and 177 ft-lbs gain AT THE WHEELS on a measured 5 psig of boost!!! The main reason the gain is so large is because up here at 5500-6000 ft altitude forced induction loses less power than naturally aspirated vehicles - hence the advantage of owning FI vehicles in Colorado
Enjoy!
EDIT: I get alot, I mean ALOT of PM's asking me about the details of my truck - specifically the TRD S/C and custom tune I have done. For purposes of my sanity and typing the same thing over and over and over, I've listed here a pretty good synopsis of my OPINION on the subject matter. Please remember this is my opinion only, and I can't be liable for mis-use, mis-interpretation or mis-information in the paragraphs below. Enjoy! 
The TRD 5.7L Supercharger kit is made especially for this engine. Many aftermarket S/C kits are piecemealed together and have marginal performance gains and cause alot of problems. TRD has taken much care/time/money to design a system from A-Z that will interface perfectly with our trucks. From an upgraded fuel system, to the top of the line blower assembly (same one found on numerous OEM offerings: Corvette ZR1, Caddy CTS-V, 2010 RR Sport S/C, Jags, etc.) to the custom tailored software management interface - This kit has it all and is one of the most fully integrated aftermarket systems money can buy. The bottom line is you will install it on your truck and never know it wasn't factory.
As far as reliability issues and potential problems go: The only issue I'm aware of (you may have read about this in the Rollcall thread) was the cold weather fuel cut issue. Basically, under a certain air intake temp, the computer would trim back fuel/throttle agressively. This bug was fixed in a software upgrade issued in July (I believe). I had it done and haven't noticed any issues since. Obviously, there are still safeguards like this in place, they are just less noticible. And for even lower air intake temps, the computer may still cut throttle/fuel marginally. There is a reason for this is to protect the engine and drivetrain. Cold air is more dense and more prone to detonation. The blower makes so much power that at very low temperatures you may be approaching the envelope of engine safety and the computer is just protecting your investment. I haven't heard of any other widespread problems or issues with this kit.
As far as tuning with aftermarket parts: If you have the kit installed at a dealership you will be covered for all parts/labor for the remainder of your factory powertrain warranty. The instant you start installing aftermarket parts like headers and a Unichip, you are risking that coverage. I'm not saying it will void your warranty, but in rare cases it could if a failure occurs that can be proven on the installation of an aftermarket part. If you look at my signature you will see that I have many of these parts installed and they do provide additional performance - especially with the supercharger, but this is the game you play if you decide to go outside OEM equipment.
My personal opinion about tuning (weather it be using a Unichip, URD MAF Controller, or other piggyback controllers) is that every aftermarket forced induction vehicle should be
professionally tuned on a chassis dyno using wideband O2 monitoring for air-fuel ratio at the very minimum. The advantages are two-fold: First, your engine is safer. Too much fuel (rich) can damage cats, waste gas, and have poor performance. Too little fuel (lean) can result in dangerously hot combustion temperatures risking crucial components in your engine, detonation (bad), and have bad performance as well. Second, you make optimum power. To play it safe, alot of aftermarket FI vendors (like TRD) will have their kits run rich - which is relatively safe for the engine, but sacrafices performance. There is a happy medium between too rich and too lean and any reputable speed shop should be able to tune your vehicle to run perfectly!
Another thing to consider when tuning is that every vehicle is different. Even if they rolled off the line with exactly the same equipment one right after the first, they are still vastly different. For the purpose of proper performance engine tuning, one of the biggest variences is in the vast variety of sensors used to provide the ECU crucial information of the combustion process. O2 sensors, mass airflow sensors, intake air temp sensors, etc. all have internal variences from one to the next - meaning that if you put two sensors side by side in action, they will most likely not read exactly the same value. This is life in mass car manufacturing. This is why one truck will run perfectly from the factory but another will run slightly rich, and another will run slightly lean. When you custom tune your vehicle you are able to dial in and/or isolate these variences (as long as the sensors provide repeatible and predictable feedback). You are basically correcting these internal variences resulting in the best power and fuel economy for a given state of modification (weather it be stock, or highly modified).
Wow - alot of info to digest. Again, I'll lay down my disclaimer: THE ABOVE ADVICE IS MY OPINION AND MY OPINION ONLY. THIS ADVICE IS TO BE USED AT YOUR OWN RISK. I ACCEPT NO RISK TO ANYONE'S VEHICLE BASED ON WHAT IS WRITTEN ABOVE.
If you have further questions about the TRD S/C, please post in this thread for the benefit of the community. If you have any further questions/concerns about URD products please contact Gadget@URD or visit www.urdusa.com. Thanks! And happy modding