Looking at the command line in the services console (services.msc) will tell you specifically where the proper .ini file is, and then you can modify that file (and hopefully get the results you want).

The command line specified for the service is shown in the Service's properties dialog. To find it:

1. Right-click on the service name
2. Click properties

Read the "Path to executable:" value. This is the command line used for the service. MySql will specify the --defaults-file option which has a path to the my.ini file.

Lowering the value is pretty trivial without a mysql restart

Let's say you want to lower timeouts to 30 seconds

First, add this to my.cnf

[mysqld]
interactive_timeout=30
wait_timeout=30

Then, you can do something like this

mysql -uroot -ppassword -e"SET GLOBAL wait_timeout=30; SET GLOBAL interactive_timeout=30"

All DB Connections after this will timeout in 30 seconds

WARNING

Make sure to use explicitly use mysql_close. I do not trust Apache as most developers do. If not, sometimes, there is a race condition where Apache closes a DB Connection but does not inform mysqld and mysqld hold that connection open until it times out. Even worse, you may see TIME_WAITs more often. Choose your timeout values wisely.

UPDATE 2012-11-12 10:10 EDT

CAVEAT

After applying my posted suggestions, create a script called /root/show_mysql_netstat.sh with the following lines:

netstat | grep mysql > /root/mysql_netstat.txt
cat /root/mysql_netstat.txt | awk '{print $5}' | sed 's/:/ /g' | awk '{print $2}' | sort -u > /root/mysql_netstat_iplist.txt
for IP in `cat /root/mysql_netstat_iplist.txt`
do
        ESCOUNT=`cat /root/mysql_netstat.txt | grep ESTABLISHED | awk '{print $5}' | grep -c "${IP}"`
        TWCOUNT=`cat /root/mysql_netstat.txt | grep TIME_WAIT   | awk '{print $5}' | grep -c "${IP}"`
        IPPAD=`echo "${IP}..................................." | cut -b -35`
        (( ESCOUNT += 1000000 ))
        (( TWCOUNT += 1000000 ))
        ES=`echo ${ESCOUNT} | cut -b 3-`
        TW=`echo ${TWCOUNT} | cut -b 3-`
        echo ${IPPAD} : ESTABLISHED:${ES} TIME_WAIT:${TW}
done
echo ; echo
netstat -nat | awk '{print $6}' | sort | uniq -c | sort -n | sed 's/d)/d/'

When you run this, you should see something like this:

[root@*** ~]# /root/ShowConnProfiles.sh
10.48.22.4......................... : ESTABLISHED:00002 TIME_WAIT:00008
10.48.22.8......................... : ESTABLISHED:00000 TIME_WAIT:00002
10.64.51.130....................... : ESTABLISHED:00001 TIME_WAIT:00000
10.64.51.133....................... : ESTABLISHED:00000 TIME_WAIT:00079
10.64.51.134....................... : ESTABLISHED:00002 TIME_WAIT:00001
10.64.51.17........................ : ESTABLISHED:00003 TIME_WAIT:01160
10.64.51.171....................... : ESTABLISHED:00002 TIME_WAIT:00000
10.64.51.174....................... : ESTABLISHED:00000 TIME_WAIT:00589
10.64.51.176....................... : ESTABLISHED:00001 TIME_WAIT:00570


      1 established
      1 Foreign
     11 LISTEN
     25 ESTABLISHED
   1301 TIME_WAIT

If you still see a lot of mysql TIME_WAITs for any given web server, here are two escalation steps to take:

ESCALATION #1

Login to the offending web server and restart apache as follows:

service httpd stop
sleep 30
service httpd start

If necessary, do this to all the web servers

service httpd stop (on all web servers)
service mysql stop
sleep 120
service mysql start
service httpd start (on all web servers)

ESCALATION #2

You can force the OS to kill TIME_WAITs for mysql or any other app with the following:

SEC_TO_TIMEWAIT=1
echo ${SEC_TO_TIMEWAIT} > /proc/sys/net/ipv4/tcp_tw_recycle
echo ${SEC_TO_TIMEWAIT} > /proc/sys/net/ipv4/tcp_tw_reuse

This will make TIME_WAITs time out in 1 second.

To give credit where credit is due...

• I got this idea from this post: How to forcibly close a socket in TIME_WAIT?
• The accepted answer has a pictorial representation of when a TIME_WAIT comes into existence.
• The answer with the idea that I liked is the one I am now suggesting.