I've done this in Mail with a combination of rules and smart folders.
The messages do indeed get sorted as I've indicated, but the smart folders also leave a copy in the main mailbox, which defeats the purpose of sorting in the first place. For example, look at the
image to the right. There are my four main accounts. My main .Mac, my
secondary .Mac, business and my wife's .Mac. Below the usual Drafts,
etc. folders, you see some of the smart folders I've made. Let's
say I get 12 messages, sorted to the folders you see in the image.
living in their new homes, they are still displayed in the "Inbox"
at the top, so now there are two representations of each message. I know that I can just set up local folders, not smart folders, and that doing so would eliminate this problem, but if I wanted to work in plain old vanilla folders, I'd use Entourage! Using Entourage would mean losing all my contacts in Address Book plus all the other benefits I listed earlier, so that's not an option. I don't mind the double linking, since I go directly to the smart folders anyway, but this experience got me thinking of how other people were using Mail's smart folders. My "including attachments" folder is a favorite, as my sisters send photos often, and the "From Home" folder holds messages from all my relatives in Pennsylvania.
So, what have you set up? Let us know.