The User Preferences dialog allows you to choose the object types for which to search. The default settings are to search for all objects, except journals and journal receivers. Unchecking an object produces a map that does not contain that object.
You can also choose to include flyover help for objects. The default is to include the flyover help.
Finally, you can show the Generate SQL dialog when generating SQL for objects. The Generate SQL dialog allows you to change your options when generating SQL. The default is to bypass the Generate SQL dialog and to display the generated SQL in the Run SQL Scripts SQL window.
These preferences are saved for each user; not each map.