http://java.com/en/download/manual.jsp
Por ejemplo, si quiero instalar silenciosamente para Internet Explorer y Firefox:
jre.exe /s IEXPLORER=1 MOZILLA=1
Command Line Install
In Java SE 6 The Windows offline installation command has the same syntax as the Windows Installation. The command is as follows:
<jre>.exe [/lang=<language ID>] [/s]
[IEXPLORER=1] [MOZILLA=1] [INSTALLDIR=<drive>:\<install_path>] [STATIC=1]
where
* <jre>.exe is the single executable installer for the Java Runtime Environment (JRE)
* /lang=<language ID>, if used, sets the localized language for the installer. For a complete list, please see Language IDs.
* /s, if used, indicates silent installation
* IEXPLORER=1, if used, indicates that the Plug-in should be registered as the default Java VM with the Internet Explorer browser
* MOZILLA=1 indicates that the Plug-in should be registered with Mozilla 1.1 and later and Netscape browsers
* INSTALLDIR, if used, specifies the drive and path of the installation
* If INSTALLDIR is not specified, the installation will go into C:\Program Files\java\jre1.6.0 (default location).
* STATIC=1, if used, specifies a static installation. This option is available in the 6u10 release and above. For more information on static install, please see Java Runtime Environment Configuration.