When you pick your config file format, think about how it will be used. Will users be editing the file in a text editor (likely Notepad-yech)? Or will they be using your web interface? The answer to these questions will determine how important it is that the format is easy to edit.

For example, some of my apps use YAML for configuration and others use Config::IniFiles. YAML is great because I can easily serialize an arbitrary data structure, but complex files are too easy to mess up if edited by hand. INI require more work to store complex structures, but they are far easier to edit by hand.

A couple of extra pointers: Remember to validate all of your configuration variables. Provide a way to create a blank/default template configuration--a newb may hopelessly mangle his configuration while editing it. If he can easily make a clean copy he will be much happier when this happens (I've been on both sides of this situation :) ).

There are plenty of great Config modules on CPAN--take a look.