Sysinternals Autoruns is the most comprehensive free Windows tool I know for managing auto starting programs. It lists the corresponding registry entries, services, drives etc. etc. (see screenshot) You can disable auto starting programs with it and can use it from the command line too. If you really want to know what is going on your computer when it boots up, then you need this tool.
However, its comprehensiveness might be its biggest disadvantage since only absolute Windows experts will know how to use it properly. Be careful to disable a program if you are not sure about its purpose.
Some time ago, I introduced a much simpler tool, Startup Control, which is sufficient if you just want to get rid of the typical auto-starting pests which are installed by so many applications these days.