For a while I've been annoyed at Mail.app's creation of the Apple Mail To Do folder on my IMAP server (I use Dreamhost). No matter what I did, it just wouldn't stay gone. There's this hint, and there are some thoughts in the comments, but no real fixes.
I returned to my problem today, and found that by going into Mail » Preferences » Composing, I was able to solve the problem. In the 'Create Notes & To Do's in:' drop-down menu, select On My Mac. Close the preferences, then delete the Apple Mail To Do folder on the server.
That's it! No more 'Apple Mail To Do' folder on the server; just locally.
Mac OS X Hints