My experience:
1. Many programs don't uninstall completely. Most security apps still don't, after all these years. I don't care if you run the mfgr's uninstall utility or do it from Add/Remove Programs -- just do a search within Regedit after uninstalling the app and you will find orphaned registry keys. There are a few security apps that do uninstall completely (NOD32 is one), but most don't. Norton doesn't. McAfee doesn't. F-Secure doesn't. I have absolutely found this to be a big problem when uninstalling one security app and then trying to install a new one. Example: You uninstall the worthless McAfee suite that came on a person's new machine and then go to install a better one. You get a message during installation of the new app that it has found another a-v app already installed and you must uninstall it before you can proceed. You've already supposedly 'deleted' McAfee via Add/Remove Programs or the McAfee uninstall utility, and you even delete the McAfee files from Program Files and within Common Files. Yet the new install is still blocked 'cuz there are still McAfee keys in the registry. I've found that running Microsoft's LiveOneCare reg cleaner (the "Clean Up scan") typically fixes the prob.
I agree with the other posts above, however, in that the LOC reg cleaner usually finds a whole slew of registry "errors," and when you click "Fix," how do you really know what all it's "fixing"? It's sort of cross your fingers and pray. The LOC reg cleaner does, however, automatically create a backup of the registry (unless you manually de-select it), so you're fine if the "fix" makes things worse in some other way.
2. Good luck getting a modern malware infection completely out of a PC just by relying on the "clean" or "fix now" feature in your security app that found the malware. If you're lucky, maybe 20-30% of the time it will work. The rest of the time, the registry will still be jacked up big-time after the security app has "removed the infection." Again, the LOC reg cleaner has worked for me in those instances.
As for everyday use not provoked by a serious problem, I'm with the other guys -- you may do more damage than just leaving it alone (or doing a fresh install).
Having said all that, I'm a huge fan of HijackThis! It often finds malicious BHOs and other gremlins, and it's probably less likely to do damage to an OS than the LOC reg cleaner IMHO. At least with HijackThis!, you can see some info about the malicious or questionable thing you're about to delete/fix. It's more precise in that respect.
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