is there a term for databases which are not system databases? Is there a term for all databases in SQL Server that are not system databases (such as master, model, tempdb)?
"User Databases".

The same "System" vs "User" distinction is also made for other objects such as tables.

For example


  Members of the db_datareader fixed database role can read all data
  from all user tables.


msdb and the distribution database (if you use replication) are also system databases that you do not mention by the way.