Here are a couple of tweaks which can improve your mysql server performance significantly. We implemented this on our hosted servers and the php/mysql queries for dynamic DB driven applications  improved by over 50%. The following are the relevant commands which can be inserted in the mysql conf file, which is normally located at /etc/my.cnf.

# Improves mysql server performance by disabling name resolution and remote mysql connections
skip-name-resolve
skip-networking

The skip-name-resolve option will disable name resolution for hostnames and the skip-networking option would disable remote connections to be made to the local MySQL server. This is a recommended setting and would improve your server security as well.

Feel free to post your queries and share any other optimisation tips as well!