I suggest Oracle Sql Developer .It's free, it's written in Java and it has support for Sql Server (you just need to add the JDBC driver from microsoft site, which it seems free too). It supports the following features: Develop,Administer,Model and migrate scenarios. It works with Oracle , MSSQL , MySQL and other providers
DBeaver is free universal database tool for developers and database administrators.
The repository contains the mysql-admin package which is a GUI tool for administrating MySQL