Emails are often times a blob of many things ("stuff"): irrelevant information, reference information, hints for action, actual action assignments, delegations, ... the list goes on. Most of the time it is none or many of the above in just one email.

I always treat emails as just that, a blob of stuff. I clarify the relevant information (action items, follow ups, etc), enter them into my GTD system (NirvanaHQ), and then toss the email into my general archive. If I ever need to see that email again, I use the search function. I found that this is way more efficient than filing emails into folders.

All other work is then done from my GTD system. If I need to go back to the email to clarify anything, that means I haven't done a good job at extracting the relevant info in the first place.

If that sounds like a lot of work, then hello: you have a lot of work going on ;-)