What makes PHP slower than Java or C#?

I'm guessing you are a little bit into the comparing of apples and oranges here - assuming that you are using all these languages to create web applications there is quite a bit more to it than just the language. (And lots of the time it is the database that is slowing you down ;-)

I would never suggest choosing one of these languages over the other on the basis of a speed argument.

One reason is the lack of a JIT compiler in PHP, as others have mentioned.

Another big reason is PHP's dynamic typing. A dynamically typed language is always going to be slower than a statically typed language, because variable types are checked at run-time instead of compile-time. As a result, statically typed languages like C# and Java are going to be significantly faster at run-time, though they typically have to be compiled ahead of time. A JIT compiler makes this less of an issue for dynamically typed languages, but alas, PHP does not have one built-in. (Edit: PHP 8 will come with a built-in JIT compiler.)