If I remember correctly I read about the TOOT-filter (or something similar) in the Doom9-forums, and if you really have three different sources to capture from, you can even use this thing to remove noise, since most probably a lot of the noise is different in the three sources (except of course for the noise, that's already been on the scanned film images), and it'll only keep the stuff that's the same in all three sources. I don't know how good this might work (and our result is already pretty clean, so I guess even this "elaborate" approach to noise reduction isn't needed). By the way, in the forum this method was used with several captures from the SAME source, which helps removing (analog) noise end errors that occured during capturing.
If you use this filter with captures from different sources, you have to scale, crop and basically line them all up PERFECTLY (down to the pixel)... I am not sure if this is possible at all, if the image is slightly rotated or skewed (might happen when scanning film images).