Did you know that you can activate a MySQL to log all queries which take a long time to run? You can use this log to identify queries which may not be optimal and could be bringing down your web application peformance. Here’s a good article on logging slow-queries on MySQL.

The slow query log is one of the less-used logs, as by default it’s not activated, but it’s a useful log for identifying queries that are not optimal. Often, in an under-performing system, especially with the default MyISAM tables (that make use of table-level locking, not row-level locking), a single query may be the cause of problems.

Link: MySQL’s Over-looked and Under-worked Slow Query Log