I think "Auto-Re" is a horrible idea. It isn't supported by current
e-mail clients for localization, nor with they strip it out when they
generate replies. It isn't supported by current e-mail processing
software, and it's encoding distinction between automatic replies and
manual ones that's already encoded in the "Auto-submitted" header.
I couldn't see our help center using it in replies to users to our
help address (trouble-ticket system) and I don't see other sites using
it either. It's biggest impact would be to make message displays more
ugly.
Also, the SHOULD use "in-reply-to" and MAY use "References" is silly.
In-Reply-To fields are enormously varied and hard to parse;
"References" fields are much better. We should definitely encourage
people to support References over In-Reply-To.
Larry