SQL: Delete Unknown Users, i.e., users not found in comments or as an author of a post. Do not use this script for community sites or sites with Subscribers.

delete-unknown-users.sql

DELETE FROM wp_users WHERE ID > 1 AND ID NOT IN (SELECT DISTINCT post_author FROM wp_posts) AND ID NOT IN (SELECT DISTINCT user_id FROM wp_comments);
DELETE FROM wp_usermeta WHERE user_id > 1 AND user_id NOT IN (SELECT DISTINCT post_author FROM wp_posts) AND user_id NOT IN (SELECT DISTINCT user_id FROM wp_comments);
DELETE FROM wp_links WHERE link_owner > 1 AND link_owner NOT IN (SELECT DISTINCT post_author FROM wp_posts) AND link_owner NOT IN (SELECT DISTINCT user_id FROM wp_comments);

DELETE FROM myprefix_users WHERE ID > 1 AND ID NOT IN (SELECT DISTINCT post_author FROM myprefix_posts) AND ID NOT IN (SELECT DISTINCT user_id FROM myprefix_comments);
DELETE FROM myprefix_usermeta WHERE user_id > 1 AND user_id NOT IN (SELECT DISTINCT post_author FROM myprefix_posts) AND user_id NOT IN (SELECT DISTINCT user_id FROM myprefix_comments);
DELETE FROM myprefix_links WHERE link_owner > 1 AND link_owner NOT IN (SELECT DISTINCT post_author FROM myprefix_posts) AND link_owner NOT IN (SELECT DISTINCT user_id FROM myprefix_comments);

For more information, see the tutorial here: http://wpsmith.net/2014/snippets/popular-wordpress-sql-user-administration-scripts/