I've read through this entire thread and as the newest guy to the forum I would like to contribute some information. I own 2 Mustangs, a 2001 Cobra with a Vortech and Aftercooler, and a 2000 Saleen Speedster with an Eaton M90. I am a power adder junkie and would like to share some real world comparisons with all of you in hopes to help you make the choice that fits your needs.
Basically the supercharger showdown is limited to these configurations:
Twin Screw, Roots, Centrifugal. All of these models are belt driven as previousley stated and cause parasetic drag (I.E. taking horsepower from the engine to create horsepower via the supercharger).
The turbo on the other hand is exhaust driven and is a totally different animal. For the sake of time and excessive wear on my keyboard we will leave this power adder out of the mix as I don't feel anyone will be using this as their power adder of choice. If you do then you certianly don't need my comments as you are most likely a fabricator and highly skilled in this department.
There will and has always been a battle between the different methods used to create supercharging technology. Manufacturers constantly battle between each other with different facts about thier system (I.E. twin screw vs. Centrifugal) and why theirs is the better choice for you. I am someone who has owned them all, installed them all, and drove them all. Below is a real world opinon and advice on what would be the best choice for the 4Runner. I have nothing to gain unlike the manufacturers by sharing my information with you.
My advice will be geared toward the owner who is looking to either tow, have great acceleration and passing power, or want's to just have a fast and fun vehichle for daily driving.
Centrifugal Sperchargers: This model is geared mainly for the person who will be using their power in the upper rpm range (Racing at the drag strip or autocross). Boost builds as the RPM's build thus creating the majority of power at the peak of your RPM range. In a real world daily driving senerio this is not the best choice for you. It's also not the best choice for towing. You will not get the full benifit of this system.
Roots/Twin Screw: These systems are somewhat similar but the twin screw design is much more efficiant. With that said let's get down to the bottom line and not debate that issue. In terms of the Eaton M90 (TRD supercharger), Boost is almost instant and will provide you with the low end torque you need to get your heavy 4Runner moving and carry it all the way to redline. It is much more practical and fun in a real world driving/towing situation as you are using everything it has to offer at the stab of the throttle. The torque peak is typically at a much lower RPM range than that of the centrifugal and in most cases will produce more overall torque when compared on a dyno assuming it is an apples to apples test.
Any of these supercharging systems will decrease your gas mileage somewhat. How much depends on your foot.

Someone looking to purchase a supercharger isn't typically worried about this as it is power we are after and not gas mileage.
Comparing my Eaton M90 supercharged Saleen to my Vortech (Centrifugal) supercharged Cobra, The Saleen wins in respect to real world daily driving conditions. It is much more fun to have on the street and actually feels like it would be faster considering the low end torque the M90 makes. It will really put you back in the seat under part to half throttle compared to my Centrifugal Cobra. The truth is my Cobra actually makes 168 more horsepower at the rear wheels and would make the Saleen a spec in the rearview mirror in an all out drag race. The Eaton M90 is very decieving under normal driving conditions and would certianly trick you into believeing that car was faster. I've done it to friends a few times.
For reference the horsepower and torque of both cars are listed below.
Saleen: 338 Rear Wheel Horsepower and 421 Rear Wheel Torque.
Cobra: 506 Rear Wheel Horsepower and 430 Rear Wheel Torque
Both cars have SAE corrected numbers using the same Dynojet.
I hope this may help some of you in understanding the difference between superchargers. If you have any further questions regarding this subject feel free to ask and I will help where I can.
Lastly, I think for the power hungry members here I may have some ideas that we may be able to use to squeeze even more horsepower out of a supercharged 4Runner. There are allot of simple things we can do to increase airflow or even boost to put us in a higer horsepower senerio. Before I go off the deep end making suggestions I would like to become a bit more familiar with the 4Runners computer, engine specs, and fuel system. The simple things are more aiflow into the intake/supercharger and better ways to get the exhaust moving out faster. Blower porting is also possible for increased horsepower and not to mention a smaller blower pulley to increase boost a bit. I have a friend who I am confident would be willing to fab up some parts for testing per my suggestions when the time is right.