Create a formula field on the cases object called "Reference"

with the following formula

"[ ref:???????.????" & SUBSTITUTE( RIGHT(Id,11) , "0", "") & ":ref ]"

Replacing the ?? with the data from one of your own ref records.

The Red ?? you can copy directly from one of your own Ref records

The Blue ?? are the first 4 of the Case ID which doesn't change

Once you've created this field you can add it to workflow email templates on the subject line and it will basicly do what SF does when you email out from a case

You can also copy  this Reference when someone sends you an offline email and forward it to your support email with the Ref pasred in the subject line and it will attach that email to your case.