Migrating from MS SQL to MYSQL is a big pain. there are no good tools to use for migration of the all the datbase objects, right from tables , data to stored procedures. We all know that Microsoft SQL server has a very good User Interface but when we come back to MYSQL we donot enjoy the same previlages as we do in SQL server.
Coming to the tools available to download for a good GUI, we have very less options, MYSQL query , PHPadmin are some of them. There are some tools which can be used to migrate the tables and data from the MSSQL to MYSQL. The MYSQL migration tool is also available to migrate the tables. But iam not sure that we can also migrate the stored procedures, but when i tried to migrate a small application i totally failed to shift the stored procedures to MYSQL. I have to migrate them manually. I have to check the syntax manually for each and every line and then execute the procedure.
There are some points which we have to keep in mind while migrating the database from MSSQL to MYSQL. The MYSQL statements has to end with semi-colon , even the ending of the for loop has to closed by a semi-colon.
When we migrate the tables from MSSQL to MYSQL we do not get the perfect script which defines the primary keys and the default values. We have to turn them on manually.
So please be carefull while doing the application and choosing the database, the migration of the database is same as a small project. 
wish you happy programmin