Thank you for writing this article!
As a technical analyst I go round and round with customers on the dangers of using a registry cleaner every week. Unless you take the time to review the stuff it is going to delete and you know what you are looking for, then my general suggestion is to avoid them.
Registry keys left behind by uninstallers that cause conflict or problems with other software are the product of poor software engineering and should be reported to the developer.
I have encountered more problems caused by registry cleaners "Cleaning" registry entries that affect everything from the personal preferences in an existing program to the registration information for a program.
The common misconception I find is that people think that their computer is "dirty" and needs to be cleaned.
There is nothing "dirty" about data.
I highly agree with CCleaner as an alternative. I don't personally use it's registry cleaning features. I just use it to delete temporary files, and clear cached files which does actually help improve the stability of many programs.
I also, use Comodo Programs Manager to monitor what changes a program makes to the system and then use that to remove the program completely. This is the safest way to cut down on bloat as it only deletes keys and files created during installation, rather than guessing at which ones are no longer needed. And it's free.
I plan on using this article to back my typical argument that registry cleaners are generally not useful or healthy for the system.