We build 3-tier enterprise solutions that typically consists of several webapp and ejbjar modules that all talk to a db and have several external integration points.
Eac
User a simple database table (Section, Key, Value). Add "Version" if you need it, and wrap the entire thing in a simple ConfigurationService class with methods like getInt(String section, String key)
Not a lot of work, and it makes the application code very neat, and tweaking with the configuration very easy.