Unless you actually want to uninstall the programs (which is a whole other issue), the only way to remove a program entirely from MSConfig's Startup list is to edit the Windows Registry.
That's an inherently dangerous job, so it's best to take precautions. Before you begin, create a System Restore point. See How to Create a Restore Point if you need instructions.
Done? Okay, let's get into the Registry Editor:
Click Start (Start>Run in XP), type regedit, and press ENTER. If you get a User Account Control message, click Yes.
Once you're in the Editor, navigate the left pane, as if it was Windows Explorer, to HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\MSConfig\startupreg.
Now it's time for another precautionary backup. But this one only protects the items that you're going to delete. In Regedit's left pane, right-click the startupreg key (a key is Regedit's equivalent of a folder), and select Export. Save the file.
Contributing Editor Lincoln Spector writes about technology and cinema. Email your tech questions to him at answer@pcworld.com, or post them to a community of helpful folks on the PCW Answer Line forum. Follow Lincoln on Twitter, or subscribe to the Answer Line newsletter, e-mailed weekly.