I use Apple Mail, and my sidebar looks like this (plus Junk, Trash etc):
Inbox — This is almost always empty. Most email I put straight into the archive.
Archive — Once I’ve dealt with the email, it goes in here.
For Later — Something to do on a rainy day, or something I’ll set a reminder for.
Notifications — My work involves regular automated status emails, and these automatically go in here. I use a mail rule for that.
Reference — Things I need to keep, like activation emails.
This system is greatly helped by the fantastic built-in search. I used to organize my email into sub-folders of Archive, but it’s hopeless to keep up with. So I thought screw it, and threw everything in one folder. I haven’t looked back, and the most time I’ll need to spend looking for something is between a couple seconds or a minute or two.