There are loads of scripts around to manage mail - check them out.
My ISP has webmail at http://webmail.maxnet.co.nz and we can colour code the messages depending on who sent or received the message as we have a wild card on 2 domains being received in the one account.
It would seem to be relatively simple to then limit the user to only see a subset also. You'd have to be prepared to get into the depths of the code though.
Personally, when we're at "home" we use Outlook and the rules in that just shove the emails around. It does mean that we have to fight for use of a single computer but it works for our situation.