On a recently launched site, I noticed that, well over the actual heavy queries on the site, the most costly request, out of several million queries, is actually SET NAMES, whic
If all queries are slow, SET NAMES can have a very low priority on the server, and therefore wait until the load dies down. If you have a lot of other queries that take a long time executing, you might want to try to optimize those first.
Another solution to this "problem", could be adding this to your my.cnf on the server:
[mysqld]
init-connect = 'SET NAMES utf8'
This makes sure the character set is set to UTF-8 when a client connects, so the client does not have to wait for the result of this "query". You probably want to disable the SET NAMES query in your software.
Mainly, I wouldn't worry too much unless you really have A LOT of SET NAMES that takes this long.