If I were doing it, I'd probably export the database to CSV and then use mysqlimport.exe or LOAD DATA INFILE to import the data. However, if you're looking for a program that'll do it for you try these:
There's a freeware version of DBTools that ought to do what you want.
MySQL-Front is no longer being developed, but ought to work. Watch out, though -- that page makes it automatically start downloading.