Just a quick on - here's how to create a virtual directory in IIS through C# code.
Update:
A better/different way to do this is documented here. The reason I say that this could be better is that it allows access to the IIS metabase via the DirectoryEntry object.
This means that I can change any of these metabase properties on a virtual directory through C#; for example, which extensions map to which DLLs. And that happens to be exactly what I was looking for :)