How can I use Mootools with Drupal 6? I am looking for a way to use Mootools with Drupal 6, without disabling jQuery, of course.
You will need to load JQuery in "noConflict mode" or MooTools in "Dollar Safe mode"; your best bet is to use "Dollar Safe mode" to avoid effecting Drupal.

See MooTools, Framework Compatibility, and Dollar $afe Mode, and The Dollar Safe Mode.