I often see comments that relate to something in the question or answer that is subsequently changed in light of the comment. This can make the comment appear odd to users who are looking at a revision of the question/answer and not the original that the comment related to. For example, a comment might point out "You wrote foo when I think you meant to put bar" and the author then corrects it. The question/answer no longer contains a reference to foo yet the comment remains and users may take a while before they realise that foo must have been removed.
How about some kind of mechanism to identify a comment with a particular revision so you can tell at a glance that it may be out of date? This could either take the form of a hard link between the comment and the revision or simply some form of shading/colour coding/other identifier to indicate that the comment relates to a previous version without necessarily indicating which one.
Assuming you don't already have a relationship between a comment and a revision logged behind the scenes, it ought to be possible to work it out for existing comments based on timestamps.