More information would be great, but in the absence of that I will assume you can do whatever you please. I'm also going to assume that these auto-replies quote the message they respond to.
As such, assuming your volume and computing power allow this, why not look for repeated responses in the ABAB pattern? That is, if you see the following, bounce it back with a kind message saying that the similarity of responses is like that generated by automatic responses:
From: Adam
Sent: Wednesday, January 03, 2013 9:10 AM
To: Box Co
Subject: RE: That thing
I'm on vacation and will get back to you on January 10.
-Adam
From: Box Co
Sent: Wednesday, January 03, 2013 9:11 AM
To: Adam
Subject: RE: That Thing
We are closed in order to observe the Tamaseseri Festival and will return tomorrow.
Box Co
Where the boxes are best!
From: Adam
Sent: Wednesday, January 03, 2013 9:10 AM
To: Box Co
Subject: RE: That thing
I'm on vacation and will get back to you on January 10.
-Adam
From: Box Co
Sent: Wednesday, January 03, 2013 9:08 AM
To: Adam
Subject: RE: That Thing
We are closed in order to observe the Tamaseseri Festival and will return tomorrow.
Box Co
Where the boxes are best!
From: Adam
Sent: Wednesday, January 03, 2013 9:07 AM
To: Box Co
Subject: That thing
Do you have that thing I put in the box?
-Adam
Do something along the lines of /\nSubject.*\n([.\n]*?)\nFrom/
to find what each party sent to each other and compare for sameness in the ABAB pattern. You'll have to remove the effects of auto-indenting etc.
This is not a simple solution, but I believe that it could be made to work and should minimize false positives and false negatives.