MSSQL is MicroSoft's SQL server. MySQL is an open-source version of that. The reason it's more popular is because it's free. Also, there was major support for PHP (also open source). You could have everything you want without having to go down the Microsoft road. What's more powerful, I really don't know. I do that if you are cheap you go with MySQL, if you are going to pay, you usually go with Oracle.
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