In Eclipse, in the menu, I can go to Window -> Preferences -> Keys and set the Scheme to \"Emacs.\" I can also click \"Export\" at the bottom-right hand side of the dialog to ex
The key configuration is relative to each workspace. You can find your configuration files at your workspace directory:
workspace /.metadata /.plugins
I haven't figured out yet which of these files corresponds to your keyboard configuration. There's also a user configuration folder at your home folder (~/.eclipse in GNU/Linux systems). You'll probably find the right file somewhere over these directories.
Something that should work is to export all preferences and then import them in the other install. But I know no way to do that for the keyboard prefs alone.
I agree that it would make sense. I suggest you open a bug report against Eclipse. Maybe it really is a missing feature (or the solution is too simple and we don't see it).
You could try exporting and importing all of your preferences
Export File->Export...->General->Preferences
Import File->Import...->General->Preferences