I abandoned Apple Mail today, at least for the time being. It having trouble synchronizing over IMAP, getting stuck and crashing on certain folders. If I drop into Offline mode I can tell the folder to rebuild itself, but this only works for a couple hours at most. Deleting local cache files didn't help. Once it got in its rut it would crash 5-10 seconds after I opened it. I don't need that sort of distraction when I'm trying to find a piece of e-mail.
I installed Thunderbird and I'm surprised how much I like it. I was never fond of the Windows version. Some of the Mac build's UI elements are noticibly non-standard and sluggish, but it's better suited to power users (subscriptions, variety of config options) and the threading is just like Mutt's: no false message acting as a thread header, and replies are indented in the tree order I'd expect.