are you talking about de-duplication, handling replies to existing case emails, or a mix? i handle replies to cases by putting the caseID in the footer of the email and then using a regex to look for it in the inbound email handler, and if found, attach an activity instead of creating a new case. if you're talking about de-deuplication, your best bet is probably going to be based on the fromaddress.
Thank you very much paul-lmi.
I found the solution at Appexchange: link
By installing this package I get the e-mail attachments as the Case Attachments (under Notes & Attachment) - which was my initial requirement.