There have been a number of tricks suggested for removing the useless Apple Mail To Do folder from your iPhone mail app. Unfortunately, none of them are true solutions because the folder gets re-created every time Mail.app is opened. After wasting an entire morning tinkering with plist files, I have something that makes the folder go away PERMANENTLY.

The important step is to go into the com.apple.mail.plist file in your ~/Library/Preferences directory, and find the ToDosMailboxName entry within your IMAP account (e.g. MobileMe) under the MailAccounts key. After exiting Mail.app, change this name to something other than "Apple Mail To Do" (I chose "Actionable"), then save and close the plist file. Then, go into the ~/Library/Mail folder and find the subfolder corresponding to your IMAP account. If you see an "Apple Mail To Do" mailbox inside this folder, move it to the trash.

That should do it (at least, it did for me). Be sure to restart your iPhone to make the folder go away on that end.