You need to identify where the bottleneck is occurring, and then attempt to remediate the problem.
- The JMeter client should be running on a well equipted machine. I prefer a Solaris/Unix server running the JVM, but for <200 threads, a modern windows machine will do just fine. JMeter can become a bottleneck, and you won't get any meaningful results once it does. Additionally, it should run on a separate machine to what your testing, and preferable on the same network. The WAN latency can become a problem if your test rig and server are far apart.
- The second thing to check is your Apache workers. Apache has a module - mod_status - which will show you the state of every worker. It's possible to have your pool size set too low. From the mod_status, you'll be able to see how many workers are in use. To few, and Apache won't have any workers to process requests, and the requests will queue up. Too many, and Apache may exhaust the memory on the box it's running on.
- Next, you should check your database. If it's on a separate machine, the database could have an IO or CPU shortage.
- If your hitting a bottleneck, and the server and db are on the same machine, you'll generally hit a CPU, RAM, or IO limit. I listed those in the order in which they are easiest to identify. If you get a CPU bound app, you can easily see you CPU usage go to 100%. If you run out of RAM, your machine will start swapping. On both Windows and unix it's fairly easy to see your available free RAM. Lastly, you may be IO bound. This too can be monitored using various tools or stats, but it's not as obvious as CPU.
Lastly, specifically to your question, the one thing that stands out is it's possible to have a huge number of session files stored in a single directory. Often PHP stores session information in files. If this directory gets large, it will take increasingly long amount of time for PHP to find the session. If you ran your test will cookies turned off, the PHP app may have created thousands of session files for each user request. On a Windows server, it will slow down faster than on a unix server, do to differences in the way directories are stored on the two operating systems.