If you really want to remove it from the registry, go to Start > Run and type regedit. First, make sure you go to file > Export to back up your current registry. If you need to restore it, just double click on the exported file and answer yes.
When you disable things in msconfig (In Windows XP) it moves the registry entry to HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\MSConfig\startupreg
Only entries you have disabled in msconfig end up here. So if you want to clean up the msconfig window when it gets too full of disabled programs. You can delete everything in this folder. Just remember, you can no longer re-enable it after you do this so make sure it's something your computer can safely function without.