Recently, I have noticed that the performance of my web sites have been pretty poor. It appeared that any pages that connected to my mysql database, were the major problem. When I looked at the output from top, I saw that the CPU usage for the VPS was reaching 100% when these performance problems were happening.
The main problem is the processes running in my VPS did not add up to using even anywhere close to that much CPU. It appears that some other VPS or the host itself was using a high processor time, and the process priority was not set correctly.
While I was trying to work around the problem, I found this page that describes a configuration for mysql that works well in a limited resource VPS. These settings seem to work for me.
Update: It looks like the problem was some other VPS, or the host. The host was rebooted, and the problem hasn't happened since