We instruct sales people to update a type field on the contact record to "former employee."
I don't know of a way to automate this, but there is the company called SiftRock which I've seen that is supposed to do something with auto replies.
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I have an intern go through and make people inactive or if they are on sabbatical, maternity leave, etc. we have a field that pauses them for a few months. We do not take the information in these replies to build up a contact database, we only use it to remove bad contacts.
My friend uses SiftRock and loves it. He works at a huge corporation so even with an intern (or 5!) it wouldn't be enough to sort through their bounce backs.