What is the "registry editing" equivalent to disabling Windows-7 startup programs with MSCONFIG

Startup programs in Windows 7 can be defined in several different locations:

• User "Start Up" folder
• System "Start Up" folder
• HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run
• HKEY_CURRENT_USER\SOFTWARE\Microsoft\Windows\CurrentVersion\Run
• and so on...

MSCONFIG, a Microsoft tool, is a good first step to disabling these startup programs that are only defined in the registry itself.

My question now is:

What is the equivalent operation when "manually" editing the registry for disabling startup programs via MSCONFIG?

I know this much ... the answer is NOT deleting entries from HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run or any other of these locations.

msconfig stores its configuration in the registry under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\MSConfig. The sub key startupreg contains information about the (location=) registry startup entries that you disabled, the sub key startupfolder contains information about the (location=) folder startup entries.