How to manage application configurations/environment variables in production

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I read some articles stating that application configs/parameters should be kept out of version control and be set as environment variables in the production environment.

My question is: How do you manage these environment variables?

Using a configuration management tool like Puppet? What if you are deploying a new version of your app and need to add some new configuration variables?

Your deploy scripts will probably also be in version control so if you set any production variable in there everyone with deploy access can see it. (and tools like Capistrano stores the deploy scripts together with application source code.)

What are the common practice for this? Thank you for your help.

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