I am not aware of functionality that allows the encryption of the entire standalone-*.xml files. Wildfly does have the capability to mask passwords in those files using the "password vault" though. Although this article is written for EAP 6, it should work just as well for Wildfly 9.
Edit: Sorry, I misread your post. You are looking for ways to encrypt things "other than datasource passwords". As I mentioned at the beginning of my reply, I'm not aware of anything. I'm sorry for providing a non-answer, but I wanted to correct my original response.