Mac OS X - disable program on startup that is not listed in Accounts' "Login items"

If it is not in the regular user Login list, then it is most likely in LaunchDaemons.

There are several locations for these, one is for Apple daemons only: /System/Library/LaunchDaemons

The others are to include 3rd party processes,
/Library/LaunchDaemons and ~/Library/LaunchDaemons.

You may also need to remove from
/Library/LaunchAgents or ~/Library/LaunchAgents

Simply remove or zip the process you don't wish to auto-launch & it should be gone at next boot.

It's also possible to use the official interface to disable a LaunchDaemon:

launchctl disable <service-name>

e.g.,

launchctl disable gui/501/com.microsoft.OneDriveLauncher

will disable Microsoft's OneDrive for the user with UID 501 (the default UID for the user created at install time; run "id" to see what your UID is).

The advantage of this method is that it disables the application for you, but not for other users of the same system, if any.

If you don't know what the service name for your application is, then run launchctl list. This shows a list of all the labels, but not the service labels; e.g., in the above example, it would show com.microsoft.OneDriveLauncher, but not the gui/501/ part. You need to add that yourself.

The man page (man launchctl) has more details.