Programs start from:
1-items in config.sys and autoexec.bat
2-Load= and Run= lines in win.ini files
3-winstart.bat file (located in the windows folder, if present)
4-Seven keys in the registry:
    HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run

    HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run

    HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunOnce

    HKEY_CURRENT_USER\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\CurrentVersion\RunOnce\Setup

    NOTE: this last key may not be on all systems, it is not on mine but I have seen posts about it.

5-Items in the startup folder
6-Items in the startup folder at
   C:\WINDOWS\All Users\Start Menu\Programs\Startup
   where C:\WINDOWS\ is your windows folder

Items 1 and 2 can be accessed by clicking start | run and then sysedit and clicking OK

Item 3 can be edited using notepad or the DOS edit program.

Item 4 can be accessed by clicking start | run and then regedit and clicking OK

Item 5 can be accessed by right clicking on start, select open from the pop-up menu, then open the programs folder, then startup.

Item 6 can be accessed using windows explorer

Items disabled using the MS Configuration program will have
rem or ; inserted in front of them in the autoexec.bat and config.sys files.
load= and run= will be changed to noload= and norun=
registry keys will be changed to run-, runservices-, runonce-, or runservicesonce-
items in the startup folders will be moved to the folder "Disabled Startup Items", without the quotes in the same folder as the startup folder.

CAUTION: you should backup any files before making any changes.