Were you having a problem that required you to make changes to the registry? If not, it is usually best to leave this alone unless you are completely familiar with the changes that are being made.
You can try to do a repair reinstall of the OS. Put your install CD in and run the install of the OS right over what is there. If that doesn't work, it is probably best to wipe the hard drive and reinstall everything from scratch. If possible, make sure you have backups of all your data before starting any of this. If you wipe the hard drive, you will lose everything. The repair reinstall should not affect the data, but sometimes computers do unexpected things.
I ran registry checker via PC Tools Registry Mechanic on my Win98SE and it stalled out at the MS Registry Checker blue screen. When I boot up it starts checking but stalls after the first line. I've tried holding down F8 and F* plus Ctrl. Nothing works. I can't use ny computer.