(APPCMD.EXE was only written for Windows Server 2008+, so it cannot apply to Windows Server 2003).
Most installations of Server 2003 have ADSUTIL.VBS which is tool that uses the ADSI automation interface of IIS. You can use that tool to do your deleting. (if for some reason that tool is not there, you can write your own script to call into ADSI to do the same).
cscript.exe %systemdrive%\inetpub\adminscripts\adsutil.vbs appdelete w3svc/1/root/MyAppName