Microsoft Windows use different places for booting processes and application. Microsoft Windows use Windows Registry, Boot.ini and Start up Menu for booting or start up applications.
To manage all start up applications is not an easy task but I will tell you an easy task. Microsoft Windows has built in utility for managing start up applications.
Open Run Command, type msconfig and press enter.
System Configuration Utility will load.
Note: Microsoft Windows 2000 does not support this utility.
After loading this utility click on Startup tab and manage all starting applications. If you want to disable any startup process then un check that process and click OK.
Windows will ask to reboot Windows. You can reboot your Windows.