When a user sends another user a message an email alert is fired with the subject and body of the message.  If the recipient replies to the message inside the community then the same original email is sent back to the originator which is a little confusing.  I would expect the email alert back to the original sender to say some like "Response to Message:xxx" and in the body have the reply and possibly the original message for reference.

I'm posting this as a question because I'm not sure if this is something that is configurable.