Why I do not see the Application Pool in my Windows 2003 IIS MMC?

If you are using Windows 2003, then you should be running IIS 6.0. If you do not  see Application Pools in the IIS MMC, it looks like you are running in IIS 5 isolation mode. You can verify this, by right clicking on “Web Sites” in the IIS MMC,  choose Properties, click on the Service tab, if “Run WWW service in IIS 5.0 isolation mode” is checked, then that is why you do not see Application Pools.  You will need to uncheck this setting and restart IIS.