StartupMonitor does not require Startup Control Panel, but it complements it nicely. When you choose not to allow a program to register itself, the program's entry becomes disabled in Startup Control Panel, so you can go back and enable it later if necessary. StartupMonitor watches the Start Menu's Startup folders and the Run entries in the registry.
StartupMonitor works on all modern versions of Windows through XP. I haven't tried it on Windows Vista yet.