Benchmark your application and database to find out where the bottlenecks are. After fixing one bottleneck (or by replacing it with a “dummy” module), you can proceed to identify the next bottleneck. Even if the overall performance for your application currently is acceptable, you should at least make a plan for each bottleneck and decide how to solve it if someday you really need the extra performance.
A free benchmark suite is the Open Source Database Benchmark, available at http://osdb.sourceforge.net/.
It is very common for a problem to occur only when the system is very heavily loaded. We have had many customers who contact us when they have a (tested) system in production and have encountered load problems. In most cases, performance problems turn out to be due to issues of basic database design (for example, table scans are not good under high load) or problems with the operating system or libraries. Most of the time, these problems would be much easier to fix if the systems were not already in production.
To avoid problems like this, benchmark your whole application under the worst possible load:
The mysqlslap program can be helpful for simulating a high load produced by multiple clients issuing queries simultaneously. See Section 5.5.8, “mysqlslap — Load Emulation Client”.
These programs or packages can bring a system to its knees, so be sure to use them only on your development systems.