Hey guys, I added this plugin and it threw a bunch of errors and stopped other JS from loading, but don't despair! I found an easy solution:
2) Place it in the wp-contents/plugins/wp-prettyphoto/js/ folder beside the existing jquery-1.3.2.min.js and name it jquery-(version number).min.js, so for jQuery 1.6.4 I would name it jquery-1.6.4.min.js
3) open wp-contents/plugins/wp-prettyphoto.php and do a find&replace for '1.3.2' to the version of your jQuery, for me I replace it with '1.6.4' and save it.
4) now your PrettyPhoto plugin is updated and no longer conflicts with your other plugins.
PROTIP: the specific line you need to change in prettyphoto.php is line #49 where it says: wp_register_script('jquery', $wpurl.'js/jquery-1.3.2.min.js', false, '1.3.2');