I use Entourage (since that's what we use in our office), and I make extensive use of Categories. Everything gets categorized by client, sometimes by project. For large projects, I create a project in the Project Center, but it hasn't really clicked for me yet, so I may not keep using it.

Right now, my inbox has about 3 or 4 emails that I can't deal with at the moment, or just simply email subscriptions I haven't read yet. (Gotta love those.)

My system was somewhat inspired by Gmail, and the way you can tag messages and then archive them to get them out of your inbox. I tag everything with a category, then move it to * Processed once I've dealt with it. That folder has everything sorted by category (client). The other folder names should be pretty self-explanatory. The blurred out one is stuff that relates to my company.

Once my 90+ Days old custom view is a decent size, I'll export that to an archive. Unfortunately, the Entourage archive doesn't retain categories. That's the only thing I don't like about this system. I picked 90 days as my cutoff point because we usually don't need to go back to stuff that's older than that.

This is still a pretty new system for me, and it gets tweaked a little every week, but I think everything is pretty clear now.

The funny thing is, I feel a weird mixture of pity and smugness when I see my co-worker's inboxes with all 1500 messages from the past year, and they just can't find that one email that they're looking for with the FTP address for Printer Z. Pity because they have their inbox so disorganized but it hasn't occured to them to organize it any other way, and smugness because I know it won't take me long to find the email about X, if I know it relates to client Y, because I can view everything for client Y instantly. It's not a lot of trouble to go ahead and tag new emails as they come in, and some of them have filters set up so I don't have to tag them manually. It just takes a lot of stress out of having to find that one email.