One thing I have recently discovered is smart folders. This makes organizing things SUPER easy and will not be affected by Mac Mail's horrible behavior (a smart folder is just like a filter applied to your existing emails), since it doesn't actually copy anything.
What you can do is set up a smart folder that filters emails in your inbox that are from you, but not sent to you. This means you were the sender, and most likely were BCC'd. One more step, show all messages from your sent folder. This will mean you have two copies of each message in the smart folder, unless your "Sent" message didn't get saved. In this case, you should be able to easily find those anomolies and copy them into your real sent folder.
I recently was looking for a way to simulate what Outlook does with AutoArchive, and I found that making a smart folder filtered on age allows me to just copy the messages from my inbox and sent items to the appropriate locally-stored folders. I still have to deal with the dreadded Mac Mail's seemingly random ability to corrupt my messages, but at least I'm not over my quota...
I think this is one of the biggest warts I've seen on my Mac since switching over last November -- I'm actually shocked this is such a long-standing problem, and it does not give me good confidence in Apple's support. I have to say, I really really like mac mail, one of the best clients I've ever used. But this one issue pretty much cancels all that out. It would be like having an iPhone that can run all the apps, but fails to make phone calls.