Here's a practice query (just to make sure we're on the right track

)
SELECT * FROM w3t_Boards
WHERE Bo_Threads = "0"
That will give you the forums that have zero topics.
Now, be sure and back up the w3t_Boards table and use this query to delete empty forums:
DELETE * FROM w3t_Boards
WHERE Bo_Threads = "0"
Warning, it will also delete your shoutbox "forum" if you have that installed... you may need to re-add it back in. I don't remember how to do an 'except' on that one
