Here’s a two good articles on optimizing and tuning MySQL databases, tables and queries.

“Even the most well-designed database, functioning on its own or as part of an application, needs to be maintained. This hour is part of a 3-hour set of administrative lessons that will give you pointers for optimizing and tuning your database so that you get the most bang for your buck. Think of your database like a garden — basic water and sunlight will allow it to grow just fine, but a little extra plant food will help it flourish.”
Link to Article: Optimizing and Tuning Your MySQL Database

“You know the scene. The database is just too slow. Queries are queuing up, backlogs growing, users being refused connection. Management is ready to spend millions on “upgrading” to some other system, when the problem is really that MySQL is simply not being used properly. Badly defined or non-existent indexes are one of the primary reasons for poor performance, and fixing these can often lead to phenomenal improvements.”
Link to Article: Optimizing MySQL: Queries and Indexes