On the SitePoint PHP blog Bruno Skvorc has a post that offers some helpful advice about optimizing your MySQL database through the use of indexes, monitoring slow queries and configuration options.

MySQL is still the world’s most popular relational database, and yet, it’s still the most unoptimized – many people leave it at default values, not bothering to investigate further. In this article, we’ll look at some MySQL optimization tips we’ve covered previously, and combine them with novelties that came out since.

He starts off with the configuration changes that can be used to optimize the database, tweaking settings for Innodb pool, handling variable inspection and using a tuning tool to determine the best settings. Next up comes the look at indexes covering the different kinds first: fulltext, descending, unique/primary and regular indexes. Finally he covers some of the usual bottlenecks seen in MySQL's use in web applications, showing how to monitor for them via the slow query log.