What is a proper or, if possible to tell, the best way to store configuration in matters of security?
So far I can tell that a database with very restricted access is a good way, but please let's exclude the database for the moment. I'm talking about things like encrypted properties files. As this is already a suggestion, I would also like to know about something like common mistakes or things I definitely have to keep in mind to acquire a secure configuration. There are already related discussions on "the best way to store configuration", however I wasn't able to find something with focus on security.
The application runs non-distributed on a host-machine, so the configuration is stored on local system. The application is, so to say, a single user application. We are talking about something like a software-firewall to be concrete. I'm actually thinking of application-scoped settings. I need data protection in a sense of privacy (I don't want to expose functionality and configuration) and integrity. I'm not afraid of an insider (admin) but more of intruders.
I already asked this question on stackoverflow but I think it is more appropriate to ask it here. I will delete the stackoverflow post in timely manner.