Slow MySql server - even on a super fast server I have just upgraded my 12 year old server to a really fast new one.  It is a dedicated server, Dell R620 1 x Intel E5-2620 (2.0GHz, 6C) CPU 32GB RAM - 4 x 250GB SSD RAID 1, in short vastly faster in every way to my old server.  However I still have a rather slow response whenever I query the MySql database.

Loading up any static is lightning fast.  Also when I view my other website (this server hosts two websites) that makes use of Mongodb, it is lighting fast.  Currently I'm only using +- 2.5Gb or ram out of the 32Gb.  Is there some setting for MySql to allow it to use more resources in order to speed up?  Alternatively is there anything else I can do (just dealing with settings or MySql queries) to speed up this slow MySql server?

The MySql version is: 5.1.73.  I'm running CentOs
I think you should change your server parameter to optimize server performance, you can go through this Percona Wizard https://tools.percona.com/wizard 

Also you can refer a blog post http://www.mysqlperformanceblog.com/2006/09/29/what-to-tune-in-mysql-server-after-installation/ this shows what parameter to consider to get optimize server performance. 

I personally recommend that you should upgrade your MySQL server to latest v5.6 GA and start using it as it has lot of optimization and InnoDB improvements.