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.

I wouldn't necessarily want this to be related to karma level - we already have a nice, colorful (and appropriately subtle) way of showing karma level, which is the karma meter.

In fact, I'd prefer that this be a personal choice, much like signatures, rather than anything automatic: it's not hard for me to make all my comments a particular shade of (say) hunter green, and let people catch on that that was my color. (I actually do this when I'm commenting within a googledoc, where we don't have real forums with identifiers. A friend of mine always chooses purple.) I would not want to see my comments appear in a red or yellow box, especially if they'd clash with the site theme.