I agree with Jan, mysqltuner.pl is a fine tool for the first tuning steps of your MySQL server.
But MySQL is part of a whole IT system. Raw performance is one thing, but what about real-life performance? (I work as an engineer at Neotys, the software vendor of NeoLoad, a load testing tool since 2005.)
To complete your test, I advise you to take a look at NeoLoad (free 30-day evaluation on www.neotys.com) to validate the performance, robustness, and scalability of your server in the context of your application. You can record and generate load from the front-end of your IT system, and measure the performance of your MySQL server when your application is actually used.
For MySQL, here are the counters that NeoLoad monitors : http://www.neotys.com/product/monitoring-mysql-web-load-testing.html.
Also, NeoLoad provides threshold values—derived from industry best practices—to raise relevant alerts.
Hervé Servy, Neotys Performance Engineer