I'll go ahead and be the voice for a PCIII .....
The reasons I prefer the Power Commander over Tuneboy.
1) It's plug and play.
2) It does not change/alter the factory settings.
3) Everything can be put back to factory by removing it.
4) Mechanics are more familiar with them and if there is a problem, see reason #3.
5) Dyno tuning is easier and there are more shops equiped to tune with them.
6) No laptop required.
7) You can make small changes with buttons right on the PCIII box itself without permanently changing the tune.
8) when it comes time to sell, putting it back factory is just taking it out.
There are probably a couple more reasons, I just have a poor memory.
Here are the cons .... (and I don't really feel they are cons, just things you do to get the same results as Tuneboy)
1) You will need to remove the secondary throttle plates.
2) A GiPro is needed to eliminate the timing retard in 1-3 gears. (and you get a gear indicator as well)
3) Tuneboy guys will give you grief.
It really all depends on what you want and how you are with wrenches and computers. Exhaust, Triples, Secondaries, GiPro and PCIII will get you the same power as Tuneboy with Exhaust, Triples and Tuneboy, so there is no sacrifice when it comes to end result power and torque. You just have to remove the throttle plates and get a GiPro in addition to the PCIII itself, the plates are free and the GiPro is $145. I would have gotten the GiPro anyway just for the gear position indicator.
I hope this helps make your decision.
jvsimons has one for sale just in case you are interested.