For the most part I have much of the install for Windows 2008 operating system and programs automated (unattended). However, one thing that I found a little more difficult to find was a command line way to turn off IE's Enhanced Security (manually turned off from Server Manager -> Configure IE ESC.
:: Backup registry keys
REG EXPORT "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Active Setup\Installed Components\{A509B1A7-37EF-4b3f-8CFC-4F3A74704073}" "%TEMP%.HKEY_LOCAL_MACHINE.SOFTWARE.Microsoft.Active Setup.Installed Components.A509B1A7-37EF-4b3f-8CFC-4F3A74704073.reg"
REG EXPORT "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Active Setup\Installed Components\{A509B1A7-37EF-4b3f-8CFC-4F3A74704073}" "%TEMP%.HKEY_LOCAL_MACHINE.SOFTWARE.Microsoft.Active Setup.Installed Components.A509B1A8-37EF-4b3f-8CFC-4F3A74704073.reg"
REG ADD "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Active Setup\Installed Components\{A509B1A7-37EF-4b3f-8CFC-4F3A74704073}" /v "IsInstalled" /t REG_DWORD /d 0 /f
REG ADD "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Active Setup\Installed Components\{A509B1A8-37EF-4b3f-8CFC-4F3A74704073}" /v "IsInstalled" /t REG_DWORD /d 0 /f
Rundll32 iesetup.dll, IEHardenLMSettings
Rundll32 iesetup.dll, IEHardenUser
Rundll32 iesetup.dll, IEHardenAdmin
REG DELETE "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Active Setup\Installed Components\{A509B1A7-37EF-4b3f-8CFC-4F3A74704073}" /f /va
REG DELETE "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Active Setup\Installed Components\{A509B1A8-37EF-4b3f-8CFC-4F3A74704073}" /f /va
:: Optional to remove warning on first IE Run and set home page to blank.
REG DELETE "HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\Main" /v "First Home Page" /f
REG ADD "HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\Main" /v "Default_Page_URL" /t REG_SZ /d "about:blank" /f
REG ADD "HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\Main" /v "Start Page" /t REG_SZ /d "about:blank" /f
This seems to work well for Windows 2008. I haven't tried it on other operating systems.