On many occasions, we see web site performance suffereing due to misconfiguration or oversight of system resources. Here is an example where RAM and Disk I/O severely impacted web site performance, and how we fixed them.
A recent project for a client who had bad site performance uncovered issues within the application itself, i.e. how the Drupal site was put together. However, overcoming those issues was not enough to achieve the required scalability with several hundred logged in users on the site at the same time.