Hi Joel,
First off, please reduce scenes when sharing them.
In this case a sphere with one of your offending textures and lights would suffice to describe your problems.
So Dr. Sassi is 100% correct in his assertion that the issue here is in the AA settings.
For starters your scene was set to geometry, this only adds AA on the edges of objects.
To demonstrate I deleted all objects but left the lights and cameras, I then went into the “top piece glossy” material and turned off all channels except for the color.
In the layer shader I disabled the overlay to produce brighter noise.
so here we have your base settings:
http://dl.dropbox.com/u/8306001/JH_base_settings.jpg
then we turn on “best” in the AA settings:
http://dl.dropbox.com/u/8306001/JH_step_01.jpg
this looks better but it is not what your noise actually looks like.
Take the threshold value from 10% and set it to 5% (If you have watched the physical renderer videos this is the same concept as the sampling explained in those videos.)
You get this:
http://dl.dropbox.com/u/8306001/JH_step_02.jpg
where did the noise go? Well now that the surface is finally getting enough samples you are seeing what your noise really looks like. Now try 2%, most of the image will now be recieving 4x4 sampling, but the results look even smoother.
http://dl.dropbox.com/u/8306001/JH_step_03.jpg
So now you go back into your noise shader and bump up the scale and you get something like this…clean predictable noise. In this case I set the noise scale to about 10%
http://dl.dropbox.com/u/8306001/JH_step_04.jpg