The program WinKey Killer v1.7 (a Windows 95 program) might work on Windows 98 -
http://majorgeeks.com/WinKey_Killer_d304.html
Otherwise, you might buy a USB keyboard of a known defective type! I'm not kidding!!
In Windows 98SE, certain keyboards cannot be recognised properly by USB, and one significant effect of the fault is that the Windows keys do not function. This might be specific to certain types of motherboard, so it is a trial-and-error suggestion.
This effect might be replicated on a non-faulty system by editing the SYSTEM.INI file in C:\WINDOWS and entering a wrong value for the keyboard driver file.
For further details, see here:
http://support.microsoft.com/kb/240022