Powershell to delete remote virtual directory  on an IIS 6.0 (Windows 2003) server (in default web site):

function delete-vDir(){
    param(
        [parameter(Mandatory = $true)][string] $vDirName,
        [parameter(Mandatory = $true)][string] $iisServer
    )
    gwmi -namespace "root\MicrosoftIISv2" -class "IISWebVirtualDir" -filter "Name = 'W3SVC/1/ROOT/$vDirName'" -ComputerName $iisServer -Authentication PacketPrivacy | %{Write-Host "Deleting vDir $vDirName on $iisServer";$_.Delete()}
}