my programs do not have files associated with them.

If you're using the old Mircosoft Regclean utility, it should have left a file that contained today's date in the file name (if I remember correctly) and the extension .reg.  Just double-click on it to undo the damage.

Download and install TweakUI from the Microsoft Powertoys pack.   Once installed this has a rebuild icons option.

Good Luck.

If asyscokid's solution doesn't work, you can also try restoring a previous registry before you did the reg clean.  If it was fairly recent, then the next thing to try is restore a previous good registry (Windows 98 keeps 5 previous backups of the registry): boot to a DOS command prompt using the Startup Menu -- which you reach after holding down the Ctrl key as the computer boots, type in the command scanreg /restore, hit the Enter key, and choose a date for the registry to restore that is prior to the problem happening.

Looks like doing a reg clean destroy some of your Windows functions. Restore a previous version of the registry.  From the Desktop, type Start > Run.  Type in scanreg /restore. Select a date of registry before you did the cleaning. Reboot. This should fix your problem.

Just to go back to my suggestion, I neglected to mention that the file you're looking for would be in the folder where the Regclean program resides.

It was a dif. program than microsoft's reg clean.It was a reg cleaner program I downloaded from  direct connect hub I can't get into any programs, even MS Dos.I get an open with box.typing in scanreg/restore in the run box does not work and typing in scanreg tells me that the resistry is fine.Is it possible that the program was a virus and can I do a win 98 re install on drive c without effecting drive D?  

So you can get to the Run box?  Then be sure there is a space between the two words in "scanreg /restore"; actually, the space is between "scanreg" and the "/".  Or you can try booting to a startup disk (download the makings for a bootdisk at www.bootdisk.com if you don't have a Win98 startup disk) and then, at the "A:/>" prompt, type the two commands:

C:
  (to change from A: to your hard drive C:)

cd\windows\command
  (to change to the directory called windows\command)
Note that in the above command there does not have to be a space between cd and \windows\command, although it works if you do put one there.

scanreg \restore
  (to start the registry checker and give you a choice of 5 backup registries to choose from)

If you choose to reinstall Windows over itself in drive C:, it will not disturb most of your programs and it will not affect drive D:.  In case it is a virus, you could try this free DOS virus checker:  F-Prot      
This free DOS-level utility lets you scan your system and files for viruses. It can detect over 50,100 viruses and Trojan horses. To target memory-resident viruses, you can load the program's definition files into memory and run the utility from two floppies.
http://www.europe.f-secure.com/download-purchase/tools.shtml

I can get to the command line and when I type in scanreg \restore I get a list of options like Restore, Fix etc. but I can't get to a place where I can choose to restore the registry to a previous one.

Thank You. That allowed me to restore the registry.Again many thanks.I got a huge headache over this.