In my experience of the most common mistakes is the failure to realise that on pretty much all Linux distros, services like Apache and MySQL come conservatively

In my experience of the most common mistakes is the failure to realise that on pretty much all Linux distros, services like Apache and MySQL come conservatively tuned. This is deliberate; it means a DoS or out-of-control process within one of those domains is unlikely to take out the entire server, because there's a hard limit on consumption of memory, CPU, child processes, threads, etc. However, this default configuration needs to be tuned to allow you to take advantage of the hardware - if you have generous hardware. Otherwise, you will wonder why your web sites are extremely unresponsive, yet the server load stands at something relatively unimpressive. I found this out the first time a blog post on one of my servers got digg'd.