Most of the Windows security updates involve over-writing and replacing .dll files, and other files that are almost continually in use by the Windows 98 operating system, which makes doing a normal DOS- or Windows Explorer-based file copy nearly impossible. (This is why you are prompted to reboot after many such updates, as that is the only way the OS can replace an 'in-use' file.) In many cases, you are also dealing with updated Registry entries, which I would certainly NOT recommend performing manually. (And doing so would end up taking longer than re-installing via download ANYWAY.)
If you still have the downloaded .zip or self-extracting executables of the updates you wish to install, I would suggest simply knocking them out all at once, one right after the other...it probably won't take as long as you think.
If you do NOT have the .zip & .exe files, and you are simply trying to bring your machine "up to snuff" with the critical security patches for Windows '98, check out the Windows Update site (www.windowsupdate.microsoft.com). It will present you with the most critical updates for your system in a reasonably easy-to-download-and-install format.
This was first published in July 2002