Unfortunately, I decided I would also back up my email locally to another directory. This is when I discovered that I hadn't emptied trash folders or compacted other folders for a while. In the process of doing that, I discovered that (a) I also hadn't emptied my separate spam folder on my personal email in a while, which is difficult to empty over IMAP, and (b) The Bat! hadn't been showing me some messages in my mailbox, which I also ascribed to The Bat! 2.x's poor IMAP support. So I switched from IMAP to POP for my personal mail, by downloading the UNIX mailbox files and importing them, which made everything marked everything as unread. I went through my inbox, filing most of it into other folders, and now my personal inbox is a lot emptier.
Then I upgraded. What I didn't realize is the upgrade included bumping up a major version to 3.x, which means it wasn't free. So now I'm on an “UNREGISTERED EVALUATION COPY” of my email client.
I was going to write about how that wouldn't be so bad, and I would consider paying again ($31.50 for Pro upgrade from previous version), but they totally nerfed threading such that my LJ mail box is totally useless—but I found where the upgrade (or dialog gnomes or something) had switched my normal view mode's “Thread by” from References to Subject. So now I get to continue to roll my eyes at people on mailing lists who don't reply with proper References headers.
I hear Thunderbird's made great strides since I last tried it, so maybe I'll try it again before I pay for more of The Bat!, but other than the threading thing and 2.x's IMAP (I haven't tried IMAP in 3.x), I'm still pretty happy with it.