Here's how it works:Edit
There will be a link in the top box on Special:Preferences that says: "Set your global preferences". That link takes you to a separate page, Special:GlobalPreferences.
GlobalPreferences will have the same structure as the regular Preferences page. There will be an extra column of checkboxes along the left side, which allow you to choose a specific preference that you'd like to set globally. Then you save your choice by clicking the Save button, as you normally do on Preferences.
There are a handful of items on the Preferences page that can't be part of GlobalPreferences: signature, gadgets, and items in Basic Information that are wiki-specific, like user groups and edit count.
You can choose to set all of the available preferences as global, but you don't have to. For the preferences that you don't specifically choose to be global, nothing will change.
On the regular Special:Preferences page, you'll see the preferences that you've chosen to be global as grayed out, with the message: "This preference has been set globally and must be modified through global preferences." You can visit GlobalPreferences to change the setting, or to remove it from your list of global preferences.
Here's a video that shows how you can switch from Preferences to GlobalPreferences, and back again.
For example: You want to see Dutch as your interface language on all wikis except for French Wikipedia, where you want to see French. Here's what you would do: navigate to Global Preferences, set Dutch as your interface language, and then check the box that makes that preference global. Then navigate to French Wikipedia, and go to your Preferences. You'll see that the global value is in effect, with a checkbox under the language preference. Check "Set a local exception for this global preference", and then you can set the French Wikipedia language to French. For all other wikis, the global preference is still in effect.
Current Special:Preferences layout
The current preferences layout, without global preferences.
Setting a global preference
Setting a global preference for 'Enable section editing by right clicking on section titles' to 'enabled.'
Local preferences, with a new "make a local exception" checkbox
You've set a global preference in Special:GlobalPreferences, and now you're looking at the local Preferences page on a wiki.
The preferences that have been set globally are grayed out, plus there's a checkbox underneath that says, "Set a local exception for this global preference."
Local preferences, with the "make a local exception" checkbox enabled
The preference is live again, and you can set it to whatever you want the local exception to be. The global preference is still set on the GlobalPreferences page.
If you uncheck this checkbox, the preference will return to the state it was in on the previous screenshot -- a grayed-out preference that shows what you've set as a global preference.
Global preference for an option with a local override
On the global preferences page, preferences with local overrides will display a relevant link.
With this approach, you can always see the preferences of the wiki that you're currently on, and if you see a preference that you want to change locally, then you can change it right there.