Drupal sites extremely slow due to cache SELECT-queries
Sounds like MySQL needs to be tuned. I would start with the InnoDB Buffer Pool Size. This answer has info on innodb_buffer_pool_size: Do Drupal websites have bad performance or are heavy?

If the innodb buffer pool is a reasonable size and If MySQL is in ball park of doing 3k+ queries per second and your running MySQL version 5.1 or lower you might be affected by the query cache bug. At work I ended up disabling the MySQL query cache after reading this bug and verifying that the version of MySQL we are running (5.1) does not have this fix http://bugs.mysql.com/bug.php?id=43758 (available in 5.5). The bug is that a lot of queries get stuck in the “freeing items” state http://dev.mysql.com/doc/refman/5.1/en/general-thread-states.html#id770305 (The thread has executed a command. Some freeing of items done during this state involves the query cache. This state is usually followed by cleaning up). I issued this command SET GLOBAL query_cache_size = 0; and saw an instant improvement in query times.