Mac Only: MailTags is a neat little add-on for Apple Mail that will help you organize your mail by tagging. It's got tons of great features and could be easily made to pull mail into your favorite productivity system. If you use Mail to manage your productivity, as many people do whether they know it or not, this is a must have.
In fact, we mentally organize mail in terms of next steps, projects, and due dates, but most email clients do not provide any way to do this: to record notes, write comments and attribute messages in the way you need. This is frustrating considering that it is your e-mail, isn't it?
MailTags is donationware ($20 suggested) and a free download for Mac OS X 10.4 Tiger. Thanks to Brian for the tip.