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 looking for.

http://wb.mysql.com/

You can see chive: http://www.chive-project.com/

or sql buddy: http://www.sqlbuddy.com/

I am not sure, there is no alternative package(GUI)better than PHPMyAdmin