Delete all tags with zero posts tagged. Can also be used to delete all tags with one post. Or other amounts … Use at your own risk. From the MySQL command line. Make sure to BACK UP YOUR DATABASE first.
DELETE a,c FROM dbname.wp_terms AS a LEFT JOIN dbname.wp_term_taxonomy AS c ON a.term_id = c.term_id LEFT JOIN dbname.wp_term_relationships AS b on b.term_taxonomy_id = c.term_taxonomy_id WHERE ( c.taxonomy = 'post_tag' AND c.count = 0 );
On the last line, you could also do
c.count < 3 which would remove all tags with less than three posts. Be creative.