I'm not sure why you would be using virtualdub with x264, it doesn't handle it well.

If you are using a good encoder like MeGUI, it automatically uses MKV.

As far as the sharpening, downloading the clips now, but what filter are you using? I'm a fan of LimitedSharpenFaster. It produces good results with little or no artifacts.

Edit: Um, I dunno. I think the clips are getting worse, not better. Comparing the deghosting scripts, the denoising scripts, the sharpening, etc. I'm seeing more and more signs of overprocessing.

Deghosting is scrubbing fine detail that isn't ghosts. Even the unsharpened 3b clip has some terrible banding (which might be a bitrate issue. Hard to say without uncompressed screenshots).

The sharpening filter is plain awful and looks like some of the official Disney BDs.

IMHO, "test4-analoclean+magicup.avi" is still the best looking clip you've posted. I can tolerate the ghosting after seeing what the filtering does.