1. PHP profilers:
Apache and Xdebug http://www.pc-freak.net/blog/tracking-php-scripts-execution-time-with-apd-and-xdebug-to-tackle-bottlenecks-in-website-performance-2/
http://pecl.php.net/package/apd
http://php.net/manual/en/apd.examples.usage.php
2. MySQL Profilers:
http://dev.mysql.com/tech-resources/articles/using-new-query-profiler.html
http://dev.mysql.com/doc/refman/5.0/en/show-profiles.html
http://myprofi.sourceforge.net/
Drupal Profilers
http://drupalperformanceblog.com/drupal-xhprof-profiling
http://pecl.php.net/package/xhprof
http://drupal.org/project/profiling
http://drupal.org/simpletest
http://drupal.org/node/79237 (Benchmarking and profiling Drupal)