EasyPG, a GnuPG interface is available from Emacs 23 which provides automatic encryption of .gpg files. You can list all the required encrypted .gpg files to be used by Emacs in a secrets.el file (for example):

;; secrets.el
(load-library "~/pass.el.gpg")

You can then load this file in your Emacs initialization file:

;; .emacs
(load "/path/to/secrets.el")

The first time you load the above, you will be prompted to create a password for the encryption. Remember it. Whenever you start Emacs thereafter, or when you try to modify the .gpg files, you will be prompted for the password.