First of all, what do we mean by good working condition? After all, the registry doesn't do any particular work, it just stores information, so when is the registry "doing well"? The answer lays in the two important functions which are performed on the Windows Registry: adding and retrieving information.
Adding and retrieving information from the registry has to be done in a timely fashion, because that information is used extensively at boot time and when installing software. A bloated registry means larger boot times and slower installation of software, which is certainly not desirable. In order for these operations to be executed with reasonable speed, the registry shouldn't be any more crowded than it needs to be, it must be kept clean.
The obvious way to do this is simply to adhere to basic system hygiene rules. You should only install applications from trusted sources and uninstall those applications that you do not use. When uninstalling applications, you should use Windows' Add/Remove Software option, or the programs own uninstaller, so as to make sure that no traces are left behind in the Registry. Using an advanced registry cleaning and optimization program like RegCure regularly is also a good idea. One scan and repair every week can work wonders.
Another thing you should consider when trying to keep the registry in good working conditions is to bring your applications up to date. Microsoft's latest developer guidelines are trying to shift the focus away from the registry, so as to make it less vulnerable to growing in size. More and more developers choose to adhere to these guidelines. As a consequence, using newer applications instead of the old versions you are used to can prove to be helpful. I know there's a tradeoff due to the way applications tend to evolve nowadays, but some things just have to be changed in the end.
In general, the only enemy of the Windows Registry is its own size. However, there are viruses which intentionally cripple the registry, so as to bring the entire system down. This calls for some extra protection against viruses and other types of malware. ParetoLogic's XoftSpySE can provide adequate protection in this case, provided that you use it to scan your system regularly.
Keeping the Windows Registry clean and in good working condition is not necessarily very difficult. Nevertheless, it does call for good habits, which some users simply refuse to learn. If it helps, try to think about your computer as if it was your kitchen. Would you fill it with rotting unwanted garbage?
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