Sometimes that which shows up in MSConfig can actually be removed by editing the registry. Sometimes. This assumes that you are using XP.
Go to HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\MSConfig
Expand startupfolder and startupreg. If you see folders there that are associated with something that you have removed delete the folder, restart, and see what that does for you.
I'd be really interested to know if you are able to remove anything.