I asked this Can I automate creating a .NET web application in IIS? a little ago, and got solutions for IIS 6 and IIS 7:
iisweb /create C:\\Rome \
You can access the IIS 5.1 metabase in VBScript, and this allows you to create a virtual directory. For example, this should set up a Virtual Directory called 'TestDir' that points to the folder C:\inetpub\wwwroot\Test
strComputer = "localhost"
strVdirName = "TestDir"
strVdirPath = "C:\Inetpub\wwwroot\Test"
set objIIS = GetObject("IIS://" & strComputer & "/W3SVC/1")
set objWebSite = objIIS.GetObject("IISWebVirtualDir","Root")
set objVdir = objWebSite.Create("IISWebVirtualDir",strVdirName)
objVdir.AccessRead = True
objVdir.Path = strVdirPath
objVdir.AppCreate (True)
objVdir.SetInfo
WScript.Echo "Successfully created virtual directory: " & objVdir.Name