There are two pre-existing questions on the site. One for Python, one for Java.
There are many libraries out there that can help you extract the reply/signature from a message:
I've also read that MailGun offers a service to parse inbound email and POST its content to a URL of your choice. It will automatically strip quoted text from your emails: http://blog.mailgun.com/handle-incoming-emails-like-a-pro-mailgun-api-2-0/
Hope that helps!