I think I am a bit of a Ninja at email and many of the things here:Recap: Becoming an Email Ninja | 43 FoldersSound ok, but there is an underlying idea that email = waste of time.
Some email is a waste of time and some is valuable.
The art is to sort it, not postpone it, avoid it or to have email free hours or days.
I use Thunderbird and use many of the features: filters, flags, and customised Labels and "Search folders". I used to have an extension called "Message Notes" but it does not work with Thunderbird 1.5. Still hoping looking for an equivalent. The sorting happens vertically into folders and what I think of as "horozontally" by multiple tags in a variety of ways.
I apply the six GTD workflow steps. Collecting; (that is easy they just arrive). Processing; most of that is automatic using the software. Organising; doing if it is under 2 min, deleting delegating, organising includes includes linking to Address books, Mind-Maps and the Calendar and thinking about the the associated NAs and alerts reminders needed. Then there is the Reviewing Doing.
As I write this I realise there is philosophy needed to do this well, GDT is part of it, "email like water" also a notion that online communication is deeply revlolutionary for the psyche. This stuff matters.