We also have this issue. I have added all of the variations of "out of office" in the Subjects To Ignore in the mail settings, but somehow my users find a way to get around this by creating unique subject lines in their automatic replies that result in 200+ new incidents generated if we aren't monitoring for them. Adding these variations to the Subjects To Ignore has helped, but some still get by.
It would be nice if there is a way to instruct Service Desk to ignore the same subject line if processed X number of times in a certain amount of time. I'm OK if a couple of incidents are processed from an automatic reply, but there should be something to break a loop if an email gets past the Subjects To Ignore.
Thanks!
Mark