Once you've installed a program on a Windows system, don't rename the program's directories or move its files from one place to another on your hard disk. If you do, your computer will likely lose track of key files. You can put your data files -- the ones you create with the application -- almost anywhere (although see Step 5). If you must change the location of an application or any of its subsidiary files, you should first uninstall the application and then reinstall it.
Never try to manually delete an application on a Windows system. Most applications make additions to system files when you install them, so it's best if the application has its own uninstall program. If an application doesn't come with an uninstall option, try the Windows 95/98/Me/XP/Vista/7 Add/Remove Programs Control Panel. If the application doesn't support the Windows 95/98/Me/XP/Vista/7 uninstall function, use an uninstaller program like Revo Uninstaller. As the Windows uninstall utility is not always reliable about removing all the pieces of an application, you may want to use an uninstall like Revo because it will do a more thorough job.
As far as registry cleaners are concerned, I don't recommend using very many of them because in general they do a poor job and may even damage your system to the point that it does not boot properly. If you are going to use a registry cleaner, use one sparingly. Programs such as RegistryEasy or CCleaner do a good job of cleaning up left-over registry entries and temporary files without removing any important ones.