When it comes to application configuration; there is no golden solution – it typically depends on your development and deployment environment.
A Configuration JSR was proposed but it is not part of JavaEE yet – http://javaeeconfig.blogspot.nl/2014/05/java-ee-config-feature-details.html.

tip If you are using JBossAS/WildFly; then this post is a good starting point https://community.jboss.org/wiki/HowToPutAnExternalFileInTheClasspath

Following approaches are typically used for application specific configuration management.

    Core Modules and property files
    Naming service (JNDI)
    System Properties
    Database configuration

caution As I said before; there is no golden rule. But storing configuration in database can be undesired especially if you are thinking about blue-green deployments.