I am trying to decide on the best way to store my applications configuration settings. There are so many options.
The majority of applications I have seen have used
It is best to do any core configuration in PHP itself, but if you are using a database and don't mind the extra overhead - you may find some flexibility in storing some settings in the database with a single extra query (assuming you organize it properly).
Either way, storing this data in JSON, INI, XL, etc is just another unneeded abstraction that is done way too much nowadays on the web. Your best bet is pure PHP, unless you like the flexibility of some settings being in the database.