brotherhood_of_LAN - 11:54 am on Nov 5, 2012 (gmt 0)
Optimising my.cnf depends a lot on whether you are primarily using InnoDB, MyISAM or a mix of these tables. It looks like you have allocated a sizeable amount of memory for both. Is that intended?
To follow on phraque's advice, inevitably it is one or more queries that are likely causing a slowness due to the nature of them (or the tables), as much as it can just be sheer volume of queries. You have a slow query log and a mysql log that can give you hints where things are going wrong.