I wrote recently about early detection for MySQL performance problems. If your server is having micro-fluctuations in performance, it’s important to know, because very soon they will turn much worse. What can you do about this?
The most important thing is not to guess at what’s happening, but to measure instead. I have seen these problems from DNS, the binary log, failing hardware, the query cache, the table cache, the thread cache, and a variety of InnoDB edge cases.