You won't get anywhere with VirtualDub's or FFDShow's filters. Nether of them are smart enough to filter the huge amounts of noise in FFVII's movies and leave any detail.
Your only hope is some very smart filtering with AVISynth, and possibly a lot of PhotoShop work. Nether of which are ever going to happen.
For instance, in the intro movie when the camera pans out over Midgar, the whole screen becomes a mass of blocks. There's not really any way to clean that very well on such a low-resolution image.
And even if you planned to tackle this, I'd highly recomend working from the PSX movies — the PC movies were re-encoded from the PSX ones, so the PSX movies are closer to the original source. You also get MUCH higher quality audio — the audio on the PC movies is HORRIBLE.
Edit: though, if I remember rightly, the PSX movies have a slight green hue for some strange reason... :/
Also, if you don't want compression artifacts in your re-encoded movies, try a lossless codec like Huffy or CorePNG. CorePNG might work well.
I might try to tackle this again at somepoint (when I have a bucket of time free). There are newer filters these days that might be used to do a somewhat decent cleanup. But like I'd get through all the movies anyway. And "serious PhotoShop work" still looms, and I suck at PS.
I think I heard that the movies are actually done in 8-bit. Urrrgh. They look better loaded into WMP.
Edit: This is because FFVII seems to skip anything modern like "post processing" or "a decent resizer" (FFVII uses point resizing, I think).
Perhaps FFVII's movies could be bettered just by doing what a media player would do for the movies: some sort of filter for some of the noise, and a bilinear resize for the movies (which would blur them out and remove a lot of the noise anyway).