To duplicate my answer on superuser....
In a domain environment you would generally use group policy for Windows settings and customised MSI installers (deployed via group policy) to alter settings for 3rd party software such as the Java runtime.
you could run this via a logon script:
REG ADD "HKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\VisualEffects" /V VisualFXSetting /T REG_DWORD /F /D 2
or set the same setting using a custom ADM in a GPO.
There is info about making a custom Java MSI with auto update disabled here:
According to the docs you can set that via group policy.
You can set user environment variables in a logon script. The command required will vary depending on the scripting language you use (cmd shell/vbs/kix)
In a DOS batch file it's just: