How can I specify the default JVM arguments for programs I run from eclipse?

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

Yes, right click the project. Click Run as then Run Configurations. You can change the parameters passed to the JVM in the Arguments tab in the VM Arguments box.

That configuration can then be used as the default when running the project.