Hmm. Mostly fine, but I do allow admins to delete comments (e.g. spam), and that'd break the numbering. Still, seems reasonable. I already provide html named anchors for #links, so I could do the phpBB thing of making the numbers also be a hyperlink straight to that comment.

Well, you could just leave gaps in the numbering.

Sure, but then I'd have to actually add an extra column to the database (the most populous table in it at that), rather than just generate it on each page view.

Can't deleted comment simply be replaced by a "comment deleted/hidden" message that maintains numbering? (plus having the kind of notice is helpful if someone somehow answered to a deleted comment).

Since you already have flavoured markdown, could you interpret a comment on entry to see if it contains a cross-reference, then store the database ID of the referant, then re-interpret it to the current number of that comment on display?

Did that make sense?

Heh. I could do that, yes. I think Circeus's approach is a lot simpler though :)