Are performance chips worthy of the hype? Are there any negative short/long term effects on the engine, transmission, supercharger, gas mileage, etc.? What about Jet performance chips?

From what people have told me, you first need to have a modified air intake, peformance exhaust and a good tune up to consider buying a chip. The chip benefits from the mods you do and maximizes its potential.

Custom pcm only offer a few advantages over stock programming.
Raised limiters; speed and revs.
Higher shift points; increased oil pressure.
Advanced timming.
This mod alone is not enough to have any gains. First you should things like intake and exhaust before adding a chip.