Cleaning

Even though Windows 98 does not come with a registry cleaner, there are ways to clean it. Your registry contains hundreds of thousands of entries, so manually cleaning is not an option. You must find a reliable program to do it for you. This can be tricky, because, of course, many programs claim to be the best. One of the more reliable registry cleaners is called "Ccleaner," which is short for "Crap Cleaner." Ccleaner has few, if any, reports of harming anyone's computer. It is updated frequently to fix bugs and keep up with changes in operating systems. Go to ccleaner.com to download the program. Install it and click the icon to run Ccleaner. When it opens go to "Registry." Leave a check next to all options and click "scan for issues. "Unused file extension" sometimes will display false positives, so you may want to leave that option unchecked. When the scan is finished, unneeded entries will be displayed. Look through the entries to see if there's anything that should be unchecked, and click "Fix selected issues." (If you're unsure just leave them all checked.) Registry cleaners are helpful, but there are times when a cleaner can't do the job. Viruses and spyware can cause so much damage that the only fix is to do a fresh Windows 98 installation.

Risks

Microsoft did not implement a pre-installed registry cleaner because the registry is not supposed to need cleaning. When a program is uninstalled, unnecessary entries are supposed to be deleted with it. Unfortunately, applications that are not written well tend to leave a mess behind. Even some of the best can leave entries behind without your knowledge. Another reason there is no registry cleaner is that tampering with the registry can be dangerous. If done incorrectly your PC could be rendered useless, requiring a complete re-install.

Source:

Crap Cleaner

Microsoft Support