Never under estimate the registry - one wrong move and you're snookered!
Windows 98 instructions for backuping up the registry (from Microsoft)
To manually back up the registry using Registry Checker
1. On the Start menu, click Run.
2. Type scanregw.exe, and click OK.
First Registry Checker verifies that the registry is structurally sound. If the registry is sound, Registry Checker offers to back it up. Registry Checker will back up the registry and store the compressed CAB file in \Windows\Sysbckup (a hidden directory).
If the registry structure is sound but a content change is keeping the computer from booting, then you need to manually restore from a backup using the following procedure.
To restore the backup manually
1. On the Start menu, click Shut Down.
2. Select Restart in MS-DOS mode and click OK.
3. At the MS-DOS command prompt, type scanreg /restore.
4. Select the latest known good backup. Backed up, compressed registry files are listed with the name Rbxxx.cab. The files show the time and date of backup. Next to each CAB file are the words Started or Not Started. Started means that the file has successfully started Windows 98, and is a known good file. Not Started means that the file has never been used to start Windows 98, so it is not a known good file.