I've been dreaming of a new kind of email client, one that only lets you look at a new email once. That's right - you get to scan it for 30 seconds and then you have to do something with it or it gets archived out of sight. And you can only look at one email at a time. I think it'd be a great way to focus on getting your inbox empty and doing something useful with each message.
Doing something would be replying to it, archiving or deleting it, creating a todo about it or sending it to a notes program for reference. I really think that last one's important: Email clients aren't for storing notes - send it somewhere else where you can link it up and annotate it more easily.
I don't have any suggestions about how to make your email client do this, but I have come up with something for making reference emails more useful, using VoodooPad.
I've been using Mail Act-On as described by Merlin Mann to quickly move messages to appropriate mailboxes, and I've been able to keep a clean inbox. But - I never bother to look at the emails I send to the reference folder. They're basically useless without more context.
I just wrote a quick script to send selected emails to voodoopad as a new page so I can link to them, add notes, and then later, search those reference emails in the same context as my notes. It's already made a big difference in how useful emails are - I can add comments to myself, find related notes in my VP doc, and since there's now a URL for every page in my VP docs, I can even link to reference emails from outside of VP - like in iGTD.
If you're interested in the script, it's here: NewVPPageFromEmail.scpt (control-click and save-as).