I would suggest using the system file checker.
You should use caution if you have installed new programs and have not used it.
It can be run by clicking start | run
Then key SFC.EXE and click OK.

If run regularly, it can spot and repair damaged files.

Don't let it restore user.exe, gdi.exe, or krnl386.exe from your windows 98 CD due to the fact that two different copies of these files exist there and it often extracts the wrong one.
The correct versions of gdi.exe and krnl386.exe are in win98_41.cab and user.exe is in win98_42.cab
There is a Microsoft Knowledge Base article at
http://support.microsoft.com/support/kb/articles/q192/8/32.asp

If you have upgraded to Windows 98 SE, you should point the system file checker to its files first.
If you have installed Internet Explorer 5, you would likely want to try restoring files from its installation files before trying to restore from the original windows 98 CD or cab files.

If you have upgraded to windows 98 SE using the update CD then user.exe is in the Win98_46.cab (it extends into the Win98_47.cab file) file on the windows 98 SE update CD.
gdi.exe is in the Win98_45.cab file and I have not been able to locate the krnl386.exe file that should be used.  The one in the mini.cab file must not be used.  It uses the same one as the original windows 98 so you can use the one in its win98_42.cab file.  You will have to manually extract it though.
I do not have access to the OEM, retail upgrade, or retail full version to check the location of those files.