Optimise InnoDB configuration:
http://dev.mysql.com/doc/refman/5.6/en/innodb-parameters.html
http://dev.mysql.com/doc/innodb-plugin/1.0/en/innodb-performance.html
http://dev.mysql.com/doc/refman/5.6/en/innodb-monitors.html
http://mysqldump.azundris.com/archives/78-Configuring-InnoDB-An-InnoDB-tutorial.html
http://www.mysqlperformanceblog.com/2007/11/01/innodb-performance-optimization-basics

Optimise queries and their index use:
http://dev.mysql.com/doc/refman/5.6/en/explain.html
http://dev.mysql.com/doc/refman/5.6/en/using-explain.html
http://dev.mysql.com/doc/refman/5.6/en/mysql-indexes.html

Use the MySQL slow query log:
http://dev.mysql.com/doc/refman/5.6/en/slow-query-log.html

Optimise MySQL memory use:
http://mysql.rjweb.org/doc.php/memory