I noticed on Frank's blog today that Adam Cogan has some suggestions for improving Microsoft software. In particular Adam has a page on improving IIS.

With all due respect to Adam, I think we have a PEBKAC issue here, not a GUI issue. Adam complains that it's difficult to distinguish between a physical folder and a virtual folder in the IIS Manager, and this makes a big difference when deleting something. To help Adam distinguish between physical and virtual directories, I have the following screenshot that compares the two.

Difference between phsyical and virtual folders

A physical folder looks like a normal Explorer folder icon. A virtual directory has a small "globe" icon superimposed on the folder.

Additionally, when you delete a virtual directory you get a warning that says "do you want to delete this item?". When you delete a physical directory you get the same message you see in Explorer when you delete an item namely: "Do you want to move -folder- and all its contents to the Recycle Bin"

Lastly, if you have an Application Root (the box with the globe) and you wish to delete that directory, then you should first remove the Application from the IIS metabase which will revert the icon back to either a physical or virtual directory. To remove the Application, bring up the properties for that directory and on the "Virtual Directory" tab click the "Remove" button.

I hope that helps your experience with the IIS Manager MMC Snapin!