Being a fervent pine user since the early nineties I was always annoyed that Debian didn't have it because of licensing issues (this time I agreed with the Debian folks though). Pine has different ways of sorting indexes of mailboxes, however, their "treaded sort" is done in a very annoying way as it sorts threads in such a way that they appear in the order of their first message. This means that old threads with a new message do not end up at the end of the index.
In addition to that it tries to be smart and "thread" even mail messages depending on the subject. This is something that does not work very well on CVS commit lists, as there are often commits to the same file while they are totally not related. This in combination with the "sort mailbox by first mail in thread first" problem is quite annoying, and it makes me miss new messages.
Pine has now been discontinued in favor of alpine - now also available in Debian as it is under the Apache 2 license. Unfortunately the old patch for Pine did not apply anymore because of rigorous refactoring of the code base. As I can not really do without nice threaded sorting I spend the weekend porting the old patch to alpine. So far, it seems to run all stable here and I am providing the patch here .
I will spend some more time on cleaning up the patch (white-space related) and then submit it to the developers and hope they want to include it in upcoming versions of alpine.