Drush users provide may provide configuration via yml files that are placed in specific directories. See our example file for more information. You may also add configuration to a site alias - see example site alias.
If you are authoring a commandfile and wish to access the user's configuration, see Command Authoring.
The Drush configuration system has been factored out of Drush and shared with the world at https://github.com/consolidation/config. Feel free to use it for your projects. Lots more usage information is there.