I like My TRD exhaust and drop in filter on my FJC. They seem to make a nice differance to me, especially the exhaust tone. I’d like to get some headers some day, but they are not going to be bolt on because the stock headers are welded into the down pipes which are welded to the cat’s. They will have to be cut off, and the new one's welded back on.
I've always found, that an exhaust system, or an intake system alone doesn't do much by it's self. But, depending on the car, if you get both and they work well together, you can see a 5-10% increase in peak HP; even more with a good port and polish.
However, there is a downside, in that you'll loose at least some low end power/torque and sometimes a lot of it depending on the setup. In a 4x4 you typically want to keep your low end power, and that’s what FJTex was talking about with lowering the rate of flow; which is true for a low RPM vehicle, especially if you want it to make lots of toque at low RPMs. High RPM vehicles, however, need the smother/easier flow so they can wrap up fast to hit peak power fast (at high RPM’s).
In other words, port and polish’s are good for high revving engines, but not for lots of low end torque like the FJC has.
The real key is to improve "efficiency", not necessarily power, with intakes and exhausts; which usually means allowing it to be louder (i.e. remove the resonators). One of the things car manufactures have to consider is the noise tolerance of their target market (not to mention the law), so usually they make them really quiet at the expense of efficiency.
So the real key is finding an exhaust system that is better tuned to your engine, not just more open and free flowing.