I second mysqltuner!
You might want to start by using one of the example config files in /usr/share/mysql. There are several to chose from depending on the system resources available. Integrate any already customized options from your existing my.cnf into the example config.
Turn off storage engines that you aren't using as well:
At this point restart mysql and let it run for a few hours; so as to have representative performance values available. Then, as was recommended previously, download and run mysqltuner.
Beyond that you may want to configure graphing of mysql performance in Munin or another graphing solution. Hard to know if any anomalies or long term trends in mysql performance exist without something like this.