I watched Merlin Mann's Google Tech Talk about processing email yesterday, and even though I'd followed his posts on Inbox Zero when they came out, it's good to get a reminder, and Merlin's an entertaining speaker - I recommend you watch it.
He talks about strategies for keeping an empty inbox based on processing email as it comes in, and deciding what to do with each message as you read it so nothing just sits there reminding you of vague, unspecified amounts of work you need to deal with sometime.
You may have to accept on faith that an empty inbox is a worthwhile goal. Some people disagree, but I think it's safe to say that for most people, moving the things you get as email into more appropriate places like notes apps, calendars or to-do lists is a great way to get in control of your work. Process it, then get to work. I've been doing this for a while, and it's a good feeling to know you don't have any surprises laying forgotten in old mail.
One point from Merlin's talk that I'd like to comment on is that email is just a medium, and it's worth thinking about whether it's really the best medium for what you're trying to do. This has been in my mind lately as I've been working on a project with a series of parallel email-based heavily technical conversations, sometimes with three or four people replying every couple of minutes. I struggle with the feeling that email is just not the best way to do this, but it seems like the only way to include everyone.
Merlin made the point that sometimes email dysfunction is just a symptom of an organizational communications problem, and no amount of email system adjustment can solve it. I agree - if you're really just tracking bugs, use a bug tracker. If you're coordinating things in real time, use IMs or IRC. If you're collaborating on a document, use something like Google Docs. Please stop overloading email.