How can I save my secret keys and password securely in my version control system?
You could use EncFS if your system provides that. Thus you could keep your encrypted data as a subfolder of your repository, while providing your application a decrypted view to the data mounted aside. As the encryption is transparent, no special operations are needed on pull or push. 
It would however need to mount the EncFS folders, which could be done by your application based on an password stored elsewhere outside the versioned folders (eg. environment variables).
I keep important settings like the hostnames and ports of development and production servers in my version control system. But I know that it's bad practice to keep secrets (like private keys and database passwords) in a VCS repository.
But passwords--like any other setting--seem like they should be versioned. So what is the proper way to keep passwords version controlled?
I imagine it would involve keeping the secrets in their own "secrets settings" file and having that file encrypted and version controlled. But what technologies? And how to do this properly? Is there a better way entirely to go about it?

I ask the question generally, but in my specific instance I would like to store secret keys and passwords for a Django/Python site using git and github.
Also, an ideal solution would do something magical when I push/pull with git--e.g., if the encrypted passwords file changes a script is run which asks for a password and decrypts it into place.

EDIT: For clarity, I am asking about where to store production secrets.