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It is really up to the developer where to save the settings. Many people have been storing values in files for years, generally .ini or something to that effect. Now xml has replaced it. I even encrypt the xml to store settings so no one can look at it and screw it up.
The majority of settings in the registry are needed for Windows so you will still need some sort of central db to query, especially for something like a right click or displaying which icon and which program opens a certain file, you don't want to query a central db just to find where the 3rd party db is then go query that.
I really think the key is promoting good development techniques, like removing your registry settings on a program uninstall, etc. Keep the registry clean and it really isn't all that bad.
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