The number of queries in show processlist when nothing is going wrong is what I'd expect. None.

It's when things are not going right that the list is important. We can see the query that's running long and probably has a table locked, backing up the whole works.

Logging slow queries would help too, you've got a few there.

14 thousand table_locks_waited is really not good.

try this script, run it from command line and see what it tells you, it's written by a MySQL developer and is a great help.

http://www.day32.com/MySQL/

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