This is new to me: the runkit extension available through PECL allows PHP functions to be redefined, and other code-level changes to be made at runtime. I came across this through the Extended Path Alias module for Drupal, which requires runkit for some functionality. The potential for this is huge: it could redefine how whole frameworks are built, allowing for core functions to be cleanly redefined instead of hooked as is currently done in Drupal.

Update: Looks like the Drupal Override Function module implements the extension. Also, the runkit_lint function validates PHP syntax (like php -l) at runtime, making eval() much more stable.