Vincent Danen recommends two Apple Mail plugins for your consideration that will give you much more granular control over how you organize and filter your email.
MailTags allows you to organize your email in a way that Apple Mail, on its own, can't. You can assign keywords to email, associate it with projects, and set priorities and deadlines. This is a great way to filter email based on this metadata by creating Smart Mailboxes that are based upon keyword or project.
Instead of moving mail around to different folders, and being limited by an email only being present in one folder at a time, you can have a mail show up in multiple Smart Mailboxes.
For instance, suppose you were working on a development project and you received an email from a user noting a bug in your software. You might give the mail the keyword "bug", and because it's a particularly nasty crash, you might give it a priority of "important." Also, since you work on many different development projects, you might associate it with the project "Software Foo." Now you have three important pieces of data that you can filter on.
Imagine a smart mailbox called "bugs" where you could look and see all emails related to bugs in any software. What if you only wanted to see mails related to "Software Foo?" Create a smart mailbox to filter on the project. And what if you decided to spend the weekend dealing with the most pressing issues, regardless of software project? You might create a smart mailbox called "Important Bugs" where it displays mails with the "bug" keyword and the "important" priority.
With regular mail filtering, that message would be in one mailbox and Apple Mail offers no way to filter messages with this kind of granularity. You would need a separate program or mechanism to track this stuff for you, rather than using email itself -- but with MailTags, you don't necessarily have to.
Mail Act-On is a companion tool that can be used with MailTags or on its own. It allows you to manipulate mail via the keyboard; move mail to different folders without using the mouse, apply filters or rules to mail via a keystroke, even multiple rules with one keystroke. This can be used to apply colors to messages and copy or move messages to certain mailboxes. Another nice feature of Mail Act-On is that it can act on outgoing messages as well, allowing you to automatically move replies or messages you wrote to particular folders. Since Apple Mail only permits rules on incoming messages, having the ability to perform actions on outbound mails can be a welcome feature.
And if you use MailTags, Mail Act-On can be used to quickly assign keywords, projects, and other MailTags metadata to messages.
There are definitely some areas that Apple Mail lacks in, particularly for mail "power" users, and this duo really helps to make Mail more useful to those who do more than just get the occasional bits of mail. There is a 30-day trial available for both programs, so it's easy enough to try them out and see if the productivity gains are worth the license costs.