A couple of days ago I discovered the following mutt config option.
set sort = threads set sort_aux = last-date-received
This means you get the usual threading but that a thread is sorted by the date the last message in the thread was received. This keeps a thread which receives new mail at the bottom of your mailbox rather than up at the top.
Another idea I found useful is to sort my spam mailbox by subject. Since a lot of SPAM has exactly the same subject it makes it really easily to quickly scan the mailbox for HAM.
You can easily do this with the following additions to your muttrc
folder-hook . set sort=threads folder-hook spam set sort=subject
You need to set the default as mutt will change the sort order when you change to the spam folder but won’t change it back when you jump out of it.