I have a web application running on Windows IIS. This app has a database where each item has a unique key (1, 2, 3...), and a list of email addresses (among other things).>
You could read in email through POP3 or IMAP using a timed script. I'm also a UNIXer so I'm struggling to comprehend how something like this is so difficult, but there you have it. Here's what I reckon you should do.
Make a script in whatever language you like. As long as it can read from POP3 or IMAP.
Have Windows run the script every 5 minutes
Have the script access the mailbox and action any emails it needs to.
My personal preference would be to install Python, but if you're limited... I don't know. ASPNET isn't bad, but I've never used it for dirty-scripting before.