Theming a custom user field on register form I have added a checkbox list field on the register form and I want to change the template for that field.

I have used field--field-checkbox-list.tpl.php and MYTHEME_field__field_checkbox-list() function, but with no luck on user_register_form.
Two possibilities.  You could alter the form element with hook_field_widget_form_alter, or you could override theme_checkbox.

More info: http://drupal.org/node/173880