The following is the setup.bat file I used to install all three MSI files.

@echo off
cls
echo iTunes Installer for Windows 7 x64
echo:
echo Installing Apple Application Support...
msiexec /i %~dp0AppleApplicationSupport.msi /qb-! /l*v %~dp0log_appleApplicationSupport.log ALLUSERS=1
echo:
echo Installing Apple Mobile Device Support...
msiexec /i %~dp0AppleMobileDeviceSupport64.msi /qb-! /l*v %~dp0log_appleMobileDeviceSupport.log ALLUSERS=1
echo:
echo Installing Apple iTunes...
msiexec /i %~dp0iTunes64.msi /qb-! /l*v %~dp0/log_iTunes64.log ALLUSERS=1 TRANSFORMS=admin.mst
echo:
echo Installation complete.

I then packaged this, the three MSI files, and the admin.mst transform file into a 7-zip self extracting installer.

Silent Un-install

MsiExec.exe /qn /X{0225AD21-F3E2-4916-BFF3-65D3F9052582}

Powershell variation for the script 

Start-Process -FilePath MSIexec -ArgumentList "/i AppleApplicationSupport.msi ALLUSERS=1 /qb-!" -Wait Start-Process -FilePath MSIexec -ArgumentList "/i AppleMobileDeviceSupport64.msi ALLUSERS=1 /qb-!" -Wait Start-Process -FilePath MSIexec -ArgumentList "/i iTunes64.msi ALLUSERS=1 TRANSFORMS=admin.mst /qb-!" -Wait

REM Remove Apple Application support
msiexec /x "{AAC5D43E-816D-4C2D-8E51-55FFF35BE301}" /QN REBOOT=ReallySuppress
REM Remove iTunes 11.1.5 x64
msiexec /x "{B8BA155B-1E75-405F-9CB4-8A99615D09DC}" /QN REBOOT=ReallySuppress

Not that hard to get a silent install, but when someone asks for some extra settings... then it gets a little problematic. But luckily there is help at hand, the trust worthy vendors have this: http://support.apple.com/kb/HT2102
Its not highly accurate, we added a lot of keys and values and it wasnt working. so, baby steps, added each reg value one at a time.. ended up with this...

Chosen settings….
[HKEY_LOCAL_MACHINE\SOFTWARE\Apple Computer, Inc.\iTunes\Parental Controls\Default]
"AdminFlags"=dword:00000b11

kParentalFlags_Locked                                 0x00000001 1
kParentalFlags_DisableExplicitContent           0x00000010 16
kParentalFlags_DisableCheckForUpdates        0x00000100 256
kParentalFlags_RestrictGames                      0x00000200 512
kParentalFlags_DisableAutomaticDeviceSync  0x00000800 2048

Total, for a decimal value for the AdminFlags of 2833

There are two separate installers for iTunes, a 32-bit version and a 64-bit version. When you visit http://www.apple.com/itunes/, you will receive the installer that matches the architecture of the OS you are currently running (as reported by your web browser).

If you need to download the installer for the other architecture (for example, you are running 64-bit Windows and you need to deploy 32-bit iTunes), visit this page:

http://www.apple.com/itunes/affiliates/download/

From here, the "Download iTunes" button will always link to the 32-bit installer, and the "Using a 64-bit edition of Windows?" link will take you to the 64-bit installer.

Unchecking 'Check for new software updates automatically' after the fact.  Copy iTunesPrefs.xml to %USERPROFILE%\AppData\Local\Apple Computer\iTunes\ (Local not Roaming).  The diff looks like this:

32c32

<               AAEAAAAAAAAAAAAAAAAAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

---

>               AAAAAAAAAAAAAAAAAAAAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA