Options that come to mind to get a list of groups in that aren't yet affiliated with a user:
1) You could add groups that aren't yet affiliated with a user through the administration widget for groups.
2) You could create a dummy user who's affiliated with your full list of groups, through whatever means you're otherwise grabbing users + their group information. (That can vary based on your security plugin...)
3) You could "hand-jam" them into the database using a SQL script. That's not at all recommended, and you should expect to be on your own, support-wise. The database structure can vary by release, hence the OWF team providing db upgrade scripts.