To manually edit the programs that Windows 98 loads at startup, users can utilize several methods. One effective approach is to use the System Configuration Utility by running "msconfig" from the Run dialog. This allows access to the Startup tab, where users can enable or disable startup items. Additionally, users can right-click on taskbar items to find a Startup option or explore program-specific options for similar settings. For further guidance, various online resources provide tips and tricks for Windows 98, including links to detailed guides.