Win98 Registry

I'd like to propose you 2 ways. First is a direct answer on yours question:

Remove a startup application
If you're trying to remove a program and can not find it in the StartUp folder (usually C:\WINDOWS\Start Menu\Programs\StartUp), then it may be launching from one of the registry keys below. To remove it, delete the value associated with the program you want to remove.

[HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run]
[HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunOnce]
[HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunServices]
[HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunServicesOnce]
[HKEY_LOCAL_MACHINE\Software\Microsoft\Windows NT\CurrentVersion\Winlogon\Userinit]

[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run]
[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\RunOnce]
[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\RunServices]
[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\RunServicesOnce]
[HKEY_CURRENT_USER\Software\Microsoft\Windows NT\CurrentVersion\Windows]

It may also be loaded from the [Load] or [Run] sections of your WIN.INI file, found in the Windows directory.
The second one will be safety. Try to use RegCleaner - all you need is to check what application you whant completly remove from the registry. You can get it from this link:
http://www.vtoy.fi/jv16/RegCleaner.exe

Good luck
Kirill