A number of applications have the handy feature of allowing users to respond to notification emails from the application. The responses are slurped back into the application.>
The best way to achieve this will be to write a window service that acts like a mail client [pop3 or imap]. This windows service should execute a timed action triggered by a timer, which connects to the mail server and polls the server for any unread message(s) available in the email inbox. The email ID to check for is the email ID on which the users will give their input on/to. If the windows service client finds that there exists any new mail(s) then it should download and filter the email body and push further for processing based on the user input in the email. You can host the input processing in the same windows service but it is not advisable to do so. The windows service can put the inputs in a special application directory or database from where your main appication can read the user inputs received in email and process them as needed.
You will be required to develop a high performance TCP/IP client for doing so. I advise you not to use the default .Net library due to performance issues, instead use one of the best availabel open source TCP/IP implementations for .Net like XF.Server from kodart. we have used this in our applications and achieved remarkably grear results.
Hope this helps..