As a developer, tools that store configuration/options in the registry are the bane of my life. I can\'t easily track changes to those options, can\'t easily port them from
Coming at this both from a user perspective and a programmers perspective I would have to say there really isn't a good exceuse to put something in the registry unless it is something like file associations, or machine specific settings.
I come from the school of thought that says that a program should be runnable from wherever it is installed, that the installation should be completely movable within a machine, or even to another machine and not affect the running of it.
Any configurable options, or required dlls etc, if they are not shared should reside in a subdirectory of the installation directory, so that the whole installation is easily moved.
I use a lot of smaller utility like programs, so if it cant be installed on a usb stick and plugged into another machine and just run, then its not for me.
I believe that Windows Registry was a good idea, but because of great abuse from application developers and standard policies not encouraged/mandated by Microsoft grew into an unmanageable beast. I hate using it for the reasons you've mentioned, there are however some occasions that it makes sense using it:
Slightly off-topic, but since I see people concerned about portability, the best approach I've ever used is Qt's QSettings class. It abstracts the storage of the settings (registry on Windows, XML preference file on Mac OS and Ini files on Unix). As a client of the class, I don't have to spend a brain cycle wondering about the registry or anything else, it Just Works (tm).
http://doc.trolltech.com/4.4/qsettings.html#details
When - You are forced to due to legacy integration or because your customer's sysadmin says "it shall be so" or because you're developing in an older language that makes it more difficult to use XML.
Why - Primarily because the registry is not as portable as copying a config file that is sitting next to the application (and is called almost the same).
If you're using .Net2+ you've got App.Config and User.Config files and you don't need to register DLL's in the registry so stay away from it.
Config files have their own issues (see below), but these can be coded around and you can alter your architecture.
(late to the discussion but) Short Answer: Group Policy.
If your customer's IT department wants to enforce settings related to Windows or the component(s) you're writing or bundling in, such as a link speed, or a custom error message, or a database server to connect to, this is still typically done via Group Policy, which makes its ultimate manifestation as settings stored in the registry. Such policies are enforced from the time Windows starts up or the user logs in.
There are tools to create custom ADMX templates that can map your components' settings to registry locations, and give the administrator a common interface to enforce policies (s)he needs to enforce while showing them only those settings that are meaningful to enforce this way.
Microsoft policy:
The registry is machine dependent. I have never liked it because its getting to slow and it is almost imposible to find the thing you need. That's why I like simple ini or other setting files. You know where they are (application folder or a user folder) so they are easy portable, and human readable.