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i se both both but mysql is the norm with PHP, you have to buy mssql or you can just use the desktop engine part of client tools al your eally need to run db from mssql
mysql is free to use but if you want to distribute it with your applications you have to buy it it syill alot cheaper than most other db engines another good free db engine is firebird also sql but totally free to use and distibute with your application.
neither is MySQL more popular nor it is widely used...it is just that it goes along well with PHP (so it is widely used with forum scripts viz. IPB and vBulletin), secondly SQL Server costs are way much higher than MySQL as Eenog said earlier. But if you see overall in the industry Oracle tops them all followed by SQL Server becuz of ther strong security features and scalability which is absent in MySQL