I agree. One of the more useful things I used comment scores for was to be sure to avoid missing useful comments that were down low on the page. Having a mechanism for setting apart well-regarded comments would be useful.
It would likely have to be normalized based on the score of the submission or the total number of comments on that submission, though, which might be more complexity than pg wants.
At the moment, a comment that's down-voted past zero becomes lighter. Perhaps very popular comments could be made more visible, or highlighted?
I think this kind of fuzzy indication of popularity might be a good compromise.