If your system is in-house and/or you have a limited number of reply formats, it's possible to do a pretty good job. Here are the filters we have set up for email responses to track tickets:
Drop all text after and including:
1. Lines that equal '-- \n' (standard email sig delimiter)
2. Lines that equal '--\n' (people often forget the space in sig delimiter; and this is not that common outside sigs)
...