I tripped across a nice little filter tonight: FFT3DGPU. It's pretty much fft3dfilter, but rewritten to off-load the work to your 3D video card.
Even on my too old system I found a pleasant bump to the speed on a project I was working on.
The only drawbacks are not everybody has a 3d card made in the past few years, and not all fft3dfilter features are incorporated yet.