Hi,
The auto response information forms part of the header, and sometime the subject and body. It all depends of the server that did the auto response.
I personally use a 3rd party component to assist with the parsing of the emails. It is called ListNanny.
It has a parser engine, and a definition file, and can assist with some additional NDR types, such as Hard and Soft Bounces, ChallengeVerification, DnsError emails, and more.
If I get an "Unknown" type back using ListNanny, I then assume it is a correct email
Hope this helps
EDIT:
After the comment. My other suggestion would be to generate a couple of different types of Auto Respond messages.
From there you view the headers of the emails manually, find any entries that might indicate that it is an Auto Respond message (which does not appear on normal message), and then write your own email parser to if an email contain any of those Auto Respond 'signature', and then flag it as such.
I can only tell you that when you start off you'll most probably have a lot of False-Positives, or Positive-False emails, but this will get better after a while, and after you've processed more emails and refined your signature.
Sorry i couldn't have been more of assistance to provide you with code samples or other ideas.