Locations of the entries in MSConfig
The enabled/checked items are populated from the following registry locations:

HKEY_LOCAL_MACHINE \ Software \ Microsoft \ Windows \ CurrentVersion \ Run
HKEY_CURRENT_USER \ Software \ Microsoft \ Windows \ CurrentVersion \ Run

-and-

HKEY_CURRENT_USER \ Software \ Microsoft \ Windows NT \ CurrentVersion \ Windows
Values named Run & Load

The disabled entries are present in these locations:

HKEY_LOCAL_MACHINE \ Software \ Microsoft \ Shared Tools \ MSConfig \ startupreg
HKEY_LOCAL_MACHINE \ Software \ Microsoft \ Shared Tools \ MSConfig \ startupfolder

(source: http://windowsxp.mvps.org/MSCONFIG.htm)