This is due to the MySQL limitations of server incapability to handle the traffic load. In order to fix this or get rid of this issues, make sure, you are doing a regular monthly or weekly maintenance of your Joomla database. Here are few tips :
- Select all tables and REPAIR tables
- Select all tables and OPTIMIZE tables
- Find out all the large tables and manipulate them to find, which can be emptied or cleaned off
- Find all the finger_terms table and empty them. This is the main reason, why Joomla 3.0 websites get really slow, when limited resources are available.