Java – Block bots by their Java referrer or User-Agent string

To disable the auto-update notification you should be able to set the dword value at HKLM\SOFTWARE\JavaSoft\Java Update\Policy\EnableJavaUpdate to 0 and HKLM\SOFTWARE\JavaSoft\Java Update\Policy\NotifyInstall to 0.

Here is a fragment from on of my startup scripts.

Option Explicit

Dim oShell
Set oShell = WScript.CreateObject("WScript.Shell")

DisableJavaUpdateNotification()

Function DisableJavaUpdateNotification
    Dim Key,Value
    Key="HKLM\SOFTWARE\JavaSoft\Java Update\Policy\EnableJavaUpdate"
    Value="0"
    oShell.RegWrite Key,Value,"REG_DWORD"
    Key="HKLM\SOFTWARE\JavaSoft\Java Update\Policy\NotifyInstall"
    Value="0"
    oShell.RegWrite Key,Value,"REG_DWORD"
End Function

There is a JAVA_TOOL_OPTIONS environment variable, that can be set in the /etc/profile.d for all users.

export JAVA_TOOL_OPTIONS=-javaagent:path/to/my-agent.jar

Every java process will then pick it up, regardless the way it is started.

From the official documentation:

This environment variable allows you to specify the initialization of tools, specifically the launching of native or Java programming language agents using the -agentlib or -javaagent options. In the following example the environment variable is set so that the HPROF profiler is launched when the application is started:

$ export JAVA_TOOL_OPTIONS="-agentlib:hprof"

This variable can also be used to augment the command line with other options for diagnostic purposes. For example, you can supply the -XX:OnError option to specify a script or command to be executed when a fatal error occurs.

There is also undocumented _JAVA_OPTIONS variable that takes precedence over the JAVA_TOOL_OPTIONS and the command line arguments, that might be handy in some cases. But because it's deprecated and might not be supported in all Java distributions it's not recommended to use.