Tracking down MySQL connection leaks

The answer seems to be adding the following entries in my.cnf under [mysqld] :

wait_timeout=60
interactive_timeout=60

I found it here (all the way at the bottom): http://community.livejournal.com/mysql/82879.html

The default wait time to kill a stale connection is 22800 seconds. To verify:

mysql> show variables like 'wait_%';
+---------------+-------+
| Variable_name | Value |
+---------------+-------+
| wait_timeout  | 60    |
+---------------+-------+

EDIT: I forgot to mention, I also added the following to my /etc/sysctl.conf:

net.ipv4.tcp_fin_timeout = 15

This is supposed to help lower the threshold the OS waits before reusing connection resources.

EDIT 2: /etc/init.d/mysql reload won't really reload your my.cnf (see the link below)

Possibly the connection pool(s) are misconfigured to hold on to too many connections and they're holding on to too many idle processes.

Aside from that, all I can think of is that some piece of code is holding onto a result set, but that seems less likely. To catch if it's a slow query that's timing out you can also set MySQL to write to a slow query log in the conf file, and it'll then write all queries that are taking longer than X seconds, default is 10 seconds.