mhthread is a Perl script which re-orders a folder's messages and annotates them, so that ExMH and the other mh/nmh commands can display them in a threaded style. It respects (and rewrites) sequences.
Note that installation requires adding some code to the ExMH user.tcl and exmh-defaults files, and that it will pack your folders (similar to folder -pack) each time it is used.
It can be downloaded from http://jmason.org/software/mhthread/ , or directly as http://jmason.org/software/scripts/mhthread.txt .