Apple’s Mail.app has some problems, but in general I like it very much. A handy feature I’ve just discovered is that you can select more than one mailbox at once, and the message list shows the union of the messages in all selected mailboxes. Handy, for example, if you want to track a conversation and see messages in chronological order from both your incoming and outgoing mail.
I also like the ‘Highlight thread of selected message’ option, which keeps the messages in their natural order but highlights those with the same subject as the one you’re currently viewing. This is much more natural for me than a fully-threaded list, though that option will also be available in the next version of OS X.