Stopping startup processes

I am trying to stop some apps that load during startup. In Win98 you could just use the msconfig command to do this. I know in W2K, you can remove programs from the Startup folder and that you can also remove programs from the Run and RunOnce in the registry. The programs I am trying to stop do not appear in either of these locations nor can I use a Group Policy to stop them. I know that you can use Task Manager to stop processes, but I don’t want to have to do this manually every day. Got any ideas?