With Windows 98, you can acheive the same affect as re-installing using the System File Checker tool.
Run SFC from the run box, and check ALL files.
When you come to a corrupt or older version file, you can select to replace the file with the one from the CD.
Next, you need to use a good registry cleaner. I have used both Norton Win Doctor, and V-COM's Fix-It.
Typically, running either utility can give you another 6 - 18 months of viable operation on a 4 year old W98 install.
Unfortunately, Windows builds up a lot of junk in the registry and system files over time.
The most effective way to clean things out is to format the hard drive, and start over.
You can reduce the pain if you can mount the drive as a slave in another system.
I have had good luck 'selectively' deleteing files from the root folder, and the Windows folders.
The primary items to leave in the Windows folders are your favorites, mail, screen savers, etc.
You will still need to re-install the applications that you use, but so long as you install them to the same folder, the updates should stay in place for them.
As a side note, I save as many Windows Update files as I can to my hard drive, and burn them onto CDs. That way, I do not have toworry about re-downloading updates.
Chas