http://www.windowsnetworking.com/articles_tutorials/Configuring-IIS-7-command-line-Appcmdexe-Part1.html
Put this into a file with .bat extension.
@echo off
appcmd start sites "site1"
appcmd stop sites "site2"
Update
Just ensure that appcmd is available anywhere by adding %windir%\system32\inetsrv\ to the PATH environment variable of your system. Alternatively, you can use the full path to appcmd.exe in the batch file.