Hi,
Are you running SBS, or a 3rd party POP3 connector for Exchange 2003, or Outlook configured to POP from 3 different POP services?
Have you looked in the header, is any information about the SMTP address it was originally sent to?
After checking the header if you find that you can see the accounts the messages where sent to, you could create a rule to do something with the message depending on the address it finds in the header, you could flag it green for one account, and another color for the others, you could even create a rule to drop messages sent to a perticular address into a specific subfolder.
Let me know how you get along with it.
Ben Hoffman
Microsoft MVP - Windows Server System Exchange