On the QaFoo blog there's a post sharing some of what they've learned about the common bottlenecks in performance testing and some things you can to do determine the issues in your own tests.

Most developers by now internalized that we should not invest time in optimizations before we know what happens exactly. [...] This is true for optimizations in your PHP code but also for optimizations regarding your infrastructure. We should measure before we try to optimize and waste time. When it comes to the assumed performance problems in your system architecture most people guess the root cause will be the database. This might be true but in most projects we put under load it proved to be false.

So, how can we figure out where the problems are located in our stack?

They talk about some common testing practices using basic tools (like ab and siege) and having them perform common operations on the application. They then talk about testing for high load, monitoring the stack for the impact and a few tools you can use to gather statistics. They end the post with a quick mention that, despite popular opinion, the issue isn't always the database's fault. Sometimes other technology that's in play - like file locking issues or processing for server-side includes - and other things that may only show up under high load.