Navicat for MySQL is hands down the best MySQL database tool. There is a free (personal)
version that does everything except transactions, stored procedures, and advanced reporting.
Its not a bad price though considering what you can do. I have been using it for years and
have always upgraded when it was time.
MySQL Workbench is very good. It's not a web-based application so it may not be what you're
I am not sure, there is no alternative package(GUI)better than PHPMyAdmin