You mean, you want to remove it from the list entirely, as opposed to just disabling it?
Well, the last tab of MSConfig tells you were to find the application you are toggling. Registry branch, if relevant, or which startup group it is in (common startup vs user-specific startup).
If you are referring to something that is 'common startup' or 'startup', and you can't figure out why it is still listed even though it is unchecked, and the application is NOT in the startup groups, check a look at this key:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\MSConfig\startupfolder\
For a list of everything that should appear in the MSCONFIG util that has been otherwise disabled. (It saves it here in case you want later to enable it).