As a GHOP Task , Cornil did a performance analysis of Drupal and found its two largest performance drains were the bootstrap process and the theming layer. Quite simply, Drupal spends too much time including code. [...] Fortunately, Drupal 7's self-learning code registry system has just landed, which should obliterate most of the wasted bootstrap cost.

Larry describes the "heart of it all", the token_get_all call, that parses through an entire PHP file, splitting out things like classes included and functions called. This is passed through a function_exists call to the current script and, if it's already there, the file isn't included repetitively.