Go to Window → Preferences → Java → Installed JREs. Select the JRE you're using, click Edit, and there will be a line for Default VM Arguments which will apply to every execution. For instance, I use this on OS X to hide the icon from the dock, increase max memory and turn on assertions:
-Xmx512m -ea -Djava.awt.headless=true
As far as I know there is no option to create global configuration for java applications. You always create a duplicate of the configuration.
Also, if you are using PDE (for plugin development), you can create target platform using windows -> Preferences -> Plug-in development -> Target Platform. Edit has options for program/vm arguments.
Hope this helps
Source: Stackoverflow.com