Gilbert after some poking around in mutt documentation, some RFCs, and some documentation (http://www.dsv.su.se/jpalme/ietf/message-threading.html
and DJB: http://cr.yp.to/immhf/thread.html
), I think that the voodoo for getting the ACS 4.2 bboard alerts to thread nicely may be the In-Reply-To headers that are set in acs-messaging/tcl/acs-messaging-procs.tcl acs_messaging_process_queue. Was going to check to see if they are in the OpenACS acs-messaging package but find that cvsweb browsing just serves errors right now. If your bboard would keep track of and send out In-Reply-To headers, it would be great!
If that is too much hassle, then using a more standard subject line convention might also work. Subject lines with "Re:" prepended to the subject line get treated properly by mutt's pseudo-thread feature but the "In Response to" additions of the current bboards mean that if I sort by subject to motor through threads, the questions get totally separated from the chain of answers.