My problems with Leopard have been kind of escalating, and I’m quickly approaching the “reinstall” advice that I’ve seen mentioned in a few support threads.
Today’s problem is this: sometime between going offline last night and plugging in my laptop this morning, I presumably deleted a message or moved a message or something, because when I plugged things in I was greeted with this dialog:
So I clicked OK, and in the background my other IMAP accounts were already starting to synchronize, but then that same dialog popped up again. I fought it off a few more times, and then Mail just hung and crashed.
I tried hunting around in ~/Library/Mail/ and tried deleting the local copy of the Drafts folder for that account, but it just came back the next time I started Mail and the problem repeated itself. It was reproducible enough that I even saw the “try starting this app with fresh preferences?” dialog for the first time (I think it was tweaked in the final version compared to the one I linked to), but for something like Mail that wasn’t exactly desirable.
My hunch was that this problem had to do with the file ~/Library/Mail/Envelope Index-journal , but it’s a nicely inscrutable binary file that I was at a loss as to what to do with it, and deleting it didn’t seem to do the trick, either.
Since I was able to start Mail while offline, I tried that and using yesterday afternoon’s Time Machine backup to attempt to restore state, but that didn’t work, either: Mail’s Time Machine implementation is specifically message oriented, so I couldn’t isolate whatever that problem was from the UI.
Ultimately, I had to move ~/Library/Mail out of the way and copy over the complete Library/Mail tree from the appropriate Time Machine backup, and that finally did the trick.
Update: Here’s an Apple Support thread: “Mail crashing”
 This theory is anecdotally confirmed by the fact that the -journal file went away once I finally got everything sorted out, though that still doesn’t explain why just deleting the -journal file didn’t resolve the problem.