Bumping that old thread, because the fight goes on.
I learned a lot about 24FPS and the absurdity it is nowadays, creating problem even for film directors ( horrible scenes in Casino Royale for example) and to high end home theater enthusiasts.
The solution I stumbled upon is called Frame Interpolation.
You need ffdshow, avisynth, MT, mvtools. Unfortunately it doesn't work with windows 7 beta as of yet (mvtools) and I'm too lazy to resinstall XP...
So I used the frame doubler in FFDshow. It's under deinterlacing. Then use the one pixel motion left and right choice.
I use Reclock and Power strip too.
It doesn't work all the time, sometimes the encoding is atrocious, but it seems it works on most of the judder problems I've had, to transform it into very slight flickering at times.
Next step would be to try realtime frame interpolation, to see if it's better or not.
Really I've been searching for months, I'm not alone with the problem, solutions aren't easy.
I even considered buying an Ati card, since their drivers are more open, which gives a better frequency control in Powerstrip.
Now the gazillions traveling scenes you have in anime (since they spare lots of frames, reducing costs) are a lot smoother.
I'll update if I find a better solution, or if problems arise.