When examining e-mails generated from Commerce (and other systems as well), you may notice a header field called "Message-ID". Sometimes, this field may include username and/or host information, for example:
 

Message-ID: <1234567890.11239485739472.JavaMail.myusername@myhost>
 

Some teams may feel a bit uneasy about this information being present in the e-mail.  Generally, WebSphere Commerce should not be setting the Message-ID field by default.  The SMTP e-mail server generates a unique ID here to uniquely identify the message.  A JavaMail API FAQ elaborates on how one can set their own Message-ID from the application.
 
Q: I set a particular value for the Message-ID header of my new message, but when I send this message that header is rewritten.
A: A new value for the Message-ID field is set when the saveChanges method is called (usually implicitly when a message is sent), overwriting any value you set yourself. If you need to set your own Message-ID and have it retained, you will have to create your own MimeMessage subclass, override the updateMessageID method and use an instance of this subclass.
 
class MyMessage extends MimeMessage {
    ...
    protected void updateMessageID() throws MessagingException {
      setHeader("Message-ID", "my-message-id");
    }
    ...
}
 
JAVAMAIL API FAQ
http://www.oracle.com/technetwork/java/faq-135477.html#msgid
 
 
I would first recommend examining the settings on your e-mail server to explore ways to modify the string at the end of the Message-ID.

Alternatively, on the Commerce side, you may potentially customize all e-mail generating commands to call this method when composing a message:

  Messaging.setContent(Integer transport, String language, Object object)
 
The third parameter takes any object that extends MimeMessage. So here, you may use a customized WCMSMimeMessage (extending MimeMessage for instance) object as above. Please note that this approach has not been tested and is not officially supported. We can only provide support at our best effort.

The Messaging object works in a similar fashion to the SendMsgCmd class (for instance, you can call similar methods such as setConfigData(), sendTransacted(), etc.).  The javadoc for this class can be found here:

Class Messaging
http://www.ibm.com/support/knowledgecenter/SSZLC2_7.0.0/com.ibm.commerce.api.doc/com/ibm/commerce/messaging/outboundservice/Messaging.html


And for SendMsgCmd info, see:

Message content setting services
http://www.ibm.com/support/knowledgecenter/SSZLC2_7.0.0/com.ibm.commerce.integration.doc/refs/rcvomin2.htm