In this recent post to his blog, Konr Ness has benchmarked the components that the Zend Framework uses to read in different types of configuration files - JSON, native PHP arrays, INI, XML and YAML files.
If you application relies on parsing one or several config files each time it is bootstrapped it is important that you select a file format that is fast to parse. But you also want to select a config file format that is easy for a human to read and edit. In a recent application I am building I also had the need to write modifications to config files, so I also benchmarked the Zend_Config_Writer components.
He includes both the sample configuration INI file and the benchmarking script he used to measure the results (all configurations were read from external files, even the native PHP option). His results were pretty predictable (with the exception of YAML reading) with the standard INI file coming in second to the native PHP arrays, but having the advantage of being more readable.