I remember in the transition between INI files and the registry (how I miss the days when applications had their own discrete text-based configuration files... oh wait, *nix still does!), and Microsoft sent out countless missives all but ordering developers to move to the registry. The registry was the approved place to store configurations, likely, I'm sure, because sticking all user settings in a single hive that could be passed around from workstation to workstation for roaming profiles.
Of course, the down side has always been that the registry just becomes cluttered with crap, particularly on a system that sees a lot of software installed, updated, reinstalled and uninstalled. Throw in there nearly two decades' worth of COM objects being incremented and decremented unsuccessfully, and a computer that's been running for five or six years, and fragmentation of the file system, and it can lead to just awful response times.