Below is the appcmd command to stop all the running sites on a IIS webserver without stopping IIS.
c:\windows\system32\inetsrv\appcmd.exe list site /xml /state:"$=started" | appcmd stop site /in
c:\windows\system32\inetsrv\appcmd.exe list site /xml /state:"$=started" | appcmd stop site /in
