Out of curiosity, why would you want to 'clean' registry?

For what it's worth...I've always considered cleaning the registry as something akin to the cure being worse then the disease. If your system is running slow, it's not the registry doing it and one mistake by you or the warz you use to clean it will effectively kill it......

I am of a different thought on cleaning and compressing the registry. It is much like any database file, every single thing installed adds junk to the registry, everything uninstalled leaves useless junk behind in the registry. Temp files leave junk in the registry and so forth.

Clean it to remove the junk, then compress it to remove the containers the junk was stored in.
System Mechanic like most registry utilities also will resolve and fix orphaned files/links or give you the option of deleting those which are not needed anymore.

http://www.knowplace.org/registry.html

WHO? Anyone who runs Windows 9x and is concerned about the size of the ever growing Win9x registry on his machine. The hints below were specifically written for single-user configurations. However, I've successfully used the suggestions here on machines with multiple-user profiles as will as single-user profile machines

WHAT? This is a novice friendly step-by-step HOWTO for CLEANING AND SHRINKING YOUR WIN9x REGISTRY. The suggestions here will allow you to compress the size of your Win9x registry without having to shell out any money to anyone.

WHY? The larger your Win9x registry gets, the longer it takes to boot your machine. Besides, there's some concern about the stability of Win9x once the registry size gets out of control. Believe it or not, since it's actually fairly simple to do this, anyone running Win9x ought to do this periodicaly as maintenance.

If you're willing to pay $20 There are a few choices. I've tried The Norton System Doctor, Reg Cleaner, System Mechanic and have settled in with Registry Healer. For my money it's the most flexible and best working registry tool.
The registry is something that needs to be maintained on a regular basis especially if you are moving, deleting, adding files & programs regularly. As someone else said it accumulates ALOT of junk and the registry has to be processed everytime you boot,so keeping it cleaned up is important.