This is not so much of a hint as a warning.
We back up and archive mail for particular projects by dragging a folder from Mail's drawer to the desktop. This folder can then be re-imported using one of the various hints on this site.
However, to my horror, we've just realised that dragging a folder out of Mail does not copy any subfolders that the folder may contain! To me, this seems really unintuitive and is not the way I would expect an Apple UI (or any UI) to work. So if you're backing up your Mail via drag-and-drop, make sure you handle any subfolders manually.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20060927085957743