Using diff and suppressing entirely different files

I have two copies of an application source code. One copy is encoded, while the other is not. There are config files scattered through-out the application's directory structure, and this is what I would like to compare.

Is there a way to use diff where-by I can ignore the wildly different files (ie: An encrypted file and an unencrypted file), and only report the difference on the similar-yet-different files (The configs).

You could write a script that uses find to find the files based on name or other criteria and file to determine whether they have the same type of contents (i.e. one compressed, one not).

For me to be more specific I would need you to give more details about whether these are parallel directory structures (files and directories appear in the same places in the two trees) and whether the files you are looking for have names that distinguish them from files you want to ignore. Any additional information you can provide might help even more.