Less Annoying CRM has a filtering option to find contacts that are not assigned to any group.  If you go to the Contacts page, there are Filters and Sorting options in the page menu on the left.  There, select “Add a filter,” and then select to filter by group.  

That will pop up a dialog with a dropdown for the filter type and a list of your group names. Select "Show contacts that are NOT in ANY group" in the dropdown, and then hit Apply Filter to see a list of contacts not in any group.  That's it! You can use this list to go through your contacts and add them to groups as appropriate.

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