I've spent years and years in pursuit of the best email management scheme. Consistently I find that the folks who are on top of their email are the folks who've adopted a scheme like this one. So, it works. It's very simple.
(1) On your email server, you configure a server-side rule that copies all incoming messages to a folder called "Archive" (I call mine "Handled" but you can call it whatever you want). Careful to make sure that it both copies the incoming message to your Archive, and also leaves it in your Inbox. Sometimes you need to resort to trickery if your email server doesn't let you make a rule that matches "Any" message. For example:
Bam, you're done. Now what happens is:
* You can delete messages from your Inbox pretty aggressively, since you have a copy in your Archive folder. The new "Show Related Messages" feature in Lion's Mail.app is really a great feature, because now you can pull up an entire thread with the press of a butan.
* All your sent mail shows up in your Inbox as well (so you don't have to sort through multiple folders to find the latest message in a thread), and in turn that means that all your sent mail is in your Archive;
* Server-side filtering means you can use any device -- including iPhones, which I don't think support mail filters -- to manage your email using the same mechanism. Just delete and move on.
* Your Inbox is all actionable, either because you need to reply or because you're waiting on a reply. You don't have to keep a message around just because.