Sorry, support for Pixel Bender (.pbk, .pbg) filters has been removed in After Effects CS6. Existing projects that use them will come in as missing effects, and saving as CS5.5 will still allow them to work when opened in CS5.5. in After Effects CS6.
Well, you now officially have 2 hardware accelerated infrastructures already in AE - OpenGL fast previews and the new 3D crap. Add to that other OpenGL and CUDA plug-ins - well, removing PB is a means of managing potential risks and conflicts. I'm sure it will reappear at some point as will other features that have been culled in CS6 when they have figured out how to do it halfway safely without messing up their already far too fragile constructs...
We'll have a full explanation up soon, but the short answer is that it took a very (surprisingly) large amount of engineering resources to maintain the Pixel Bender infrastructure. We have limited engineering resources. We found that we could do a lot more good by spending those resources on other features.
We talked to every deleoper of Pixel Bender plug-ins for AFter Effects before making this decision, and most of them are willing to use the C/C++ SDK to make plug-ins, instead. Pixel Bender plug-ins were somewhat easier to write, but they were much slower and also didn't have as many features as those written with the C/C++ SDK.
I think one of the main points of Pixel Bender was, that everybody could code
some quick'n'dirty tool and use it right within After Effects. There have been
a lot of new, simple tools that where never created when SDK was around.
It's really sad that this possibility disappears now. If you want to let people
move to the SDK I hope you will provide really simplified wizards and an
excellent development UI integration. Not having a C/C++ background makes
it almost impossible to set up everything correctly to compile for example
a simple color transformation plugin with GPU acceleration.
Nevertheless it would be a miracle if PB gets released as Open Source,
from the amount of feedback this would be an excellent solution keeping
and even extending the possibilities of todays complex production pipelines.