* Using registry to store preferences makes moving settings of some application from one PC to other a pain.
* Using registry to store preferences makes saving a version of settings of some application, and restoring them later, annoying.
* Using registry to store preferences gives an application enough rope to hang itself so properly, that advanced registry surgeon skills are necessary to get it running again.
However, I think that currently on MS desktop OSs, it is just too complicated and too easily broken, for the amount of goodness it brings. Sadly, due to all the application legacy, many of the issues will be unfixable in the foreseeable future.
For some reason, I see nothing wrong with good old plain text config files, for application specific settings. They're robust, simple, and easily fixed when things go wrong. For OS settings, maybe some centralized DB is necessary, to allow the applications to access it in controlled manner.
But, IMHO the biggest fail with registry, is the fact that it's the system and user configurations mixed together. It's just too hard to tell things apart after they've taken the blender round together.
I shall end my thread de-railing efforts now, as I'm actually interested to see quality discussion on the topic at hand.