Skimming over JWZ's document, I have latched onto the "references" bit, ignoring the In-Reply-To altogether. If you're interested in the full source, please /msg me -- the caveat (and reason why it hasn't been posted before) is that the reader itself is rather incomplete -- it retrieves, sorts & displays them, but doesn't store messages or message pointers.

# sorting by oldest first seems to give the best chance for accurate m
+essage threading.
        # I apologize for the nasty parens nesting scheme as well.
        foreach (sort {
                        Date_Cmp ( $messages{$a}{"date"}, $messages{$b
+}{"date"})
                      } keys %messages
                ) 
        {
            my $ref = $messages{$_}{"references"};            
            print STDERR "Checking $_ for references -- $ref --\n";
            # getrefs runs through all the messages in placed, 
            # looking for references within the current message
            my $childof=get_refs($ref, \%placed);           
            #
            #   if the current message is a child of another,
            #   nest it to that messages' node, otherwise place as a c
+hild of 
            #   the newsgroup node.
            #
            #   In either case, we add it to the list of messages we'v
+e 'placed'.
            #   'placed' is a bad analogy, and should be replaced.
            if ($childof){
                $placed{$_}=$this->AppendItem ($placed{$childof}, $_."
+ ".$messages{$_}{"subject"});                
            } else {
                $placed {$_}=$this->AppendItem ($item,$_." ".$messages
+{$_}{"subject"});
            }
            print STDERR "I have ". keys (%placed) . " items\n";
        }
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and the sub get_refs,

    sub get_refs {    
        my $msg_refs = shift;
        my $msg_list = shift;
        my @parent_refs =reverse split /\s+/, $msg_refs;
        foreach my $aref(@parent_refs) {
            print STDERR "\tChecking $msg_refs\n";
            if (exists $$msg_list{$aref}){                    
                print STDERR "$_ is child of $aref\n";
                return $aref;
            }
        }            
        return undef;
    }
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