I'm writing this entry in the hopes of helping some other poor soul that runs into this problem. While trying to migrate a friends Wordpress MySQL data I got the following error when trying to import the dump file into a new server.

#1065 - Query was empty

I just did a standard mysqldump to convert the database into text. No special options. However, for some reason the MySQL client on my web host is inserting comments and headers into the dump file. When trying to import the dump file, MySQL is choking on the comments. Remove the comments and headers, and the script works fine. This was with v5.0.x of MySQL. I'm using PHPMyAdmin to do the import.

I'm sure there is some "obvious" command line option to fix this. But at this point, I just don't care. It was easier just to remove the comments and move down the road.