Slow MySql Server Performance - What and How to check?
Log slow queries- If your system has a ton of queries, it gets tougher to find out which queries are slowing your system. MySQL provides a tool to log slow queries for further analysis
http://dev.mysql.com/doc/refman/5.0/en/slow-query-log.html
EXPLAIN Extended command shows details about your queries when your have no idea what is happening http://dev.mysql.com/doc/refman/5.0/en/explain-extended.html
To speed up your queries use Index - A good practice is add index by seeing which fields are in the WHERE clause add index for them.
Also if you are retrieving all fields from a table, the query gets slower by fetching all data from disk. In SELECT query you should specify which fields you need to bring instead to bring them all with *
Make use of Query Cache http://dev.mysql.com/doc/refman/5.1/en/query-cache-configuration.html
Make sure that your MySQL server configuration file options are optimized according to your hardware
http://dev.mysql.com/doc/refman/5.5/en/option-files.html
Make sure that you are using optimized data types while creating a table structure 
For example "Comments" fields has size of 256 characters, reply it to MYSQL with a field with type VARCHAR(256) instead of using TEXT. The query will be much faster.


Procedure_Analyse() can help you in finding optimal data types:

http://www.mysqlperformanceblog.com/2009/03/23/procedure-analyse/

http://dev.mysql.com/doc/refman/5.0/en/procedure-analyse.html


There are open source tools from Percona - http://www.percona.com/software/percona-toolkit which can be helpful for MySQL DBA's and specially those who are new to MySQL these tools will provide good assistance to them.