Quite a few years ago (when the sizes of HDD's was low and their costs were high), I and some others over on the Doom9 forum experimented with converting (MPEG-2) DVD's with their non-square (anamorphic) pixels to square pixel (MPEG-4) encodes. This involved working out the original pixel height of the movies image area, cropping away any black mattes followed be re-sizing the pixel width of the movies image area... Overall the experiment worked well and the resulting encodes looked good.
Nowadays however, because HDD's are so large and pretty cheap, there's less of a need to do any encoding at all. Indeed, most of us just extract the MPEG-2 'movie only' part the original DVD and don't perform any encoding at all...