Perhaps a box around the comment, or background shading, or font color…? Maybe related to karma level?
When I first saw this page title in my email, I assumed it was going to be a comment rating scheme (which I think would be awesome — allowing users to promote comments that are the most helpful and draw the eye of incoming googlers looking for answers, for example; also being able to affect appearance of a page based on it's rating would be a sweet feature).
As to preserving a site maker's ability to create their own schemes, I'd recommend making alterations by shades of the webmaster's chosen schemes rather than letting just any new color in. It's one thing when it's just in a forum, but when comments are per page, that could really draw a clash.
Alternatively, add the ability to ignore custom color selections, or choose from presets about how to treat them in the admin:manage module.