Windows has a multitude of places where applications or commands can run on startup.
There's folders, registry entries etc. there are so many places that msconfig has a Startup tab to try to show you some of them in one place.
You mention in the comment you want to have something start when a certain user logs in... and to save messing around with the registry then I would suggest creating a shortcut in the path:
This will vary depending on what version of Windows you are using. The folder you are looking for is the "startup folder" though for that user irrespective of Windows version.
If you wanted to do this from the command line then you could pipe your command into a batch file for instance or even use the Windows registry command line tools to add an entry to the registry's "Hive Key Current User" (HKCU) under HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run\