I have some apps running in IIS. All of them were visible in Performance Monitor: ASP.NET Applications.
I wanted to test the Error event counter, and moved my application files to other folder. Now when I copied back the app, it doesn't appear in the list of apps to monitor.
After copying back your application, you need to restart your application and send a request to wake up the application. Then you should be able to see the asp.net application instance in performance monitor.