General rule: use config files for anything local
Specific rule: Use a configuration file format that can represent complex data
That’s right, I’m looking at you, .ini and .properties files.
Use something like YAML, or XML, or even straight programming-language code (i.e., a file with a PHP hash or a perl hashref or whatnot) that can actually represent, in a logical way, the complexities of the stuff you need to configure. And then, again, have a singleton class that will read that data and expose it in a useful and safe way.
And include a semantics checker if you can manage to write one. It’ll save everyone a load of trouble.
Huge bonus points if your configuration singleton class can read from multiple files, overriding previous (default) definitions with subsequent (local) ones.