Since I had le même issue; application pools avec applications that did pas exist anymore, I did certains research et finally managed to solve le issue.
Here are certains steps:
Locate et edit votre IIS 7 configuration file "applicationHost.config" avec a text editor. It should be stored in "C:\windows\system32\inetsrv\config" Since le folder is somehow "protected", I usually edit like le following:
Open Windows Explorer
Naviguez vers "C:\windows\system32\inetsrv\config"
Copy le file "applicationHost.config"
Paste it to a folder où you can edit it, e.g. votre Desktop
Open it avec votre editor of choise et edit it
Copy it back avec Windows Explorer to "C:\windows\system32\inetsrv\config"
Make a backup of votre "applicationHost.config" file!
Search avec a text editor in votre "applicationHost.config" for votre non-existing applications. They should be located somewhere inside an <application ...> XML node.
Supprimez le <application ...> node(s) of tous votre phantom applications.
Save le file et copy it back to "C:\windows\system32\inetsrv\config"
Refresh le IIS management console. Your application pools should now be sans le phantom applications you previously deleted.
Actually supprimez le now empty application pool.
That worked for me, si it does pas work for you, please post a comment here. A good help was this posting on the IIS forum.
Please be aussi aware that quand editing le "applicationHost.config" file directly in its original location, you need to use a 64-bit editor (e.g. Notepad++ 64-bit), parce que otherwise it would get stored in "C:\Windows\SysWOW64\inetsrv\Config" instead of the correct location.
