The best way is from the configuration menus of the application you want to stop running at startup. To do this, double click on its system tray icon or launch it using its shortcut. Then, search for the Preferences, Options, Settings or Configuration menus. For example, Preferences is generally found under the Edit menu, while Options under Tools. However, there are exceptions to this rule.
Once you found the configuration menus of the application, search for options such as 'Start [application name] on system/computer startup', 'Launch [application name] on Windows startup'. When found, uncheck those options and click OK or Apply.
Warning: be careful with configuration options such as 'Always show tray icon' or anything related to showing the tray icon. By unchecking these settings you won't stop the application from running at startup. You will only hide its tray icon. The application will continue to run at each Windows startup.
Another method is to use the System Configuration Utility and disable them from there. To learn how to do this, check our tutorial called How to configure your startup programs.