StartUp Items
There are several places that this information can be stored; they are described below:
StartUp Folder
The StartUp Folder is located under your Start Menu in a program group named "StartUp".  Any items located in the StartUp Folder are represented by a corresponding shortcut icon within this program group.  The physical location of the StartUp Group is usually directly under the Windows folder, within the "Start Menu" folder.
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run
Startup items stored in this location of your registry are automatically started when the current user only is logged in.  On systems with multiple user accounts, this information may change depending on who is logged in, however this is most applicable on systems connected to a network and most prevalent under Windows NT.
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\RunOnce
Startup items stored in this location are handled exactly the same as the previous location, except that items are only run one time and then automatically removed.
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run
Startup items stored in this location of your registry are automatically started each Windows session no matter who is logged in.
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunOnce
Startup items stored in this location are handled exactly the same as the previous location, except that items are only run one time and then automatically removed from the list of startup items.
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunOnceEx
Startup items stored in this location of your registry are automatically started each Windows session no matter who is logged in.
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunServices
Startup items stored in this location of your registry are automatically started as "Services" (most applicable under Windows NT), which are programs intended to start before any other programs are loaded and to continue running even after the system is "locked".
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunServicesOnce
Startup items stored in this location of your registry are automatically started as "Services", but only started once and then removed from the list of startup items automatically.  Services, which are most applicable under Windows NT, are programs intended to start before any other programs are loaded and to continue running even after the system is "locked".
Win.ini
The "Win.ini" file is an initialization file that stores configuration data for your system and is processed at the beginning of each Windows session.  Within this file are two sections where applications can be added in order to have then automatically load when Windows starts.  Both the "Load" and "Run" sections operate in basically the same way as far as this tool’s purpose is concerned:  They store a path and filename which is interpreted by Windows as instructions to launch that file upon startup.
All User’s StartUp Folder
Windows NT, 2000, XP, or later contain a special folder for startup files that instructs the operating system to load these items when Windows boots, regardless of who is logged into the machine.  Any files, documents, or applications placed in the All Users’ StartUp Folder will be subject to these conditions and load independently of the current user.
Config.sys
Under Windows 95, 98, and Me, Config.sys is a small file usually located on the root folder of your bootable drive (or drive partition).  It contains rudimentary startup and driver information that is processed before Windows begins loading.  Any items placed in this file must be applicable to the Windows 95/98/Me pre-load process or they will be ignored.  The Config.sys file is processed before the Autoexec.bat file described below.
Autoexec.bat
Under Windows 95, 98, and Me, Autoexec.bat is a small file usually located on the root folder of your bootable drive (or drive partition).  It contains rudimentary startup information that is processed before Windows begins loading.  Any items placed in this file must be applicable to the Windows 95/98/Me pre-load process or they will be ignored.