Well, taking the simplest approach here and filtering based on the properties returned from your given example, I would probably opt to use the site identifier portion in the Name property:
Get-WmiObject IIsWebVirtualDir -namespace "ROOT\MicrosoftIISv2" | `
Where-Object { $_.name -like "W3SVC/1/*" }
The above example only shows virtual directories on the default website that is set up with IIS first install. This always has the identifier 1.
Note: the backtick ` after the bar is the line continuation character (actually it's the escape character, but I'm escaping the EOL,) like _ in Visual Basic. I'm using this so the ugly horizontal scrollbars don't show up in the code block above.
-Oisin