This has been driving me crazy! An aside-Why am I seeing four copies? If I then view my inbox on an iPad, however, I'll see four copies of that message in the inbox! If I then delete them all from the iPad, the pesky original message will then be removed from the inbox on the Mail.app. I'll archive it again, and it'll again return sometime later. I'll archive a message, only to see it return 10 minutes later. I've been having awful problems recently with Mail.app's ability to delete and archive messages in my inbox. Problems archiving and deleting inbox messages On the other hand, that MBA does contain an extensive set of Smart Mailboxes, most of which search for messages containing certain tags.
On the MacBook Air that I use at home and at work, I have a simple set of four rules that apply account-specific colors to incoming messages. Many of those rules involve the application of tags to messages, via the wonderful MailTags plugin. I run Mail.app on an internet-hosted Mac mini, in order to provide server-side spam filtering and to pre-process my email based on an extensive set of rules.
