Abhinav Singh has a recent post to his blog looking at three extensions that you can use to help understand the inner workings of the core Zend Engine.
"PHP tokens and opcodes" - When a PHP script is executed it goes through a number of processes, before the final result is displayed. These processes are namely: Lexing, Parsing, Compiling and Executing. In this blog post, I will walk you through all these processes with a sample example. In the end I will list some useful PHP extensions, which can be used to analyze results of every intermediate process.
He touches on the steps the average PHP script takes in its processing - lexing, parsing/compiling and the actual execution of the opcodes. The tokenizer, parsekit and VLD (Vulcan Logic Disassembler) extensions can help you get down into the nuts and bolts of the language and the engine that makes it work.