Best practices for setting the environment variables for a custom build application?

I did built a custom app that integrate another system into the Zendesk UI for our company.

The application is working very well and I'm getting ready to deploy it into the production environment.

There are few variables that hold connection information that will need to switch between values based on the environment where it is deployed.

Those variables holds url's for web services, database connection strings, logging setup...

I would like to know if there are best practices for setting and managing those  environmental variables to be easy to deploy the app in different environment?