Get rvkroots.exe (Google), extract updroots.exe from it and put it in some folder. Get Curl and unpack in the same folder. Then you just run the following batch file:
curl -O http://www.download.windowsupdate.com/msdownload/update/v3/static/trustedr/en/authroots.sst
curl -O http://www.download.windowsupdate.com/msdownload/update/v3/static/trustedr/en/delroots.sst
curl -O http://www.download.windowsupdate.com/msdownload/update/v3/static/trustedr/en/disallowedcert.sst
curl -O http://www.download.windowsupdate.com/msdownload/update/v3/static/trustedr/en/roots.sst
curl -O http://www.download.windowsupdate.com/msdownload/update/v3/static/trustedr/en/updroots.sst
updroots authroots.sst
updroots updroots.sst
updroots -l roots.sst
updroots -d delroots.sst
updroots -l -u disallowedcert.sst
Done, takes 20 seconds to update, no complicated nonsense like they do elsewhere on the internet. ;)
You need Updroots.exe from one of the unofficial SP’s for 98SE or ME. It is inside ROOTSUPD.cab in UMECU105A.