custom attribute configuration

@paul pointed me in the right direction, but was actually incomplete in version 1.7.0.2

I had to extend an addition method _prepareValues in my Setup.php file

<?php
class AtlanticBT_Featured_Model_Resource_Eav_Mysql4_Setup
   extends Mage_Eav_Model_Entity_Setup
{
    protected function _prepareValues($attr)
    {
        $data = parent::_prepareValues($attr);
        $data = array_merge($data, array(
                'apply_to' => $this->_getValue($attr, 'apply_to'),
            )
        );

        return $data;
    }

    public function getDefaultEntities()
    {
        return array(
                'catalog_product' => array(
                    'entity_model'      => 'catalog/product',
                    'attribute_model'   => 'catalog/resource_eav_attribute',
                    'table'             => 'catalog/product',
                    'additional_attribute_table' => 'catalog/eav_attribute',
                    'entity_attribute_collection' => 'catalog/product_attribute_collection',
                    'attributes' => array(
                        'featured' => array(
                            'group'                      => 'General',
                            'type'                       => 'int',
                            'backend'                    => '',
                            'frontend'                   => '',
                            'label'                      => 'Featured',
                            'input'                      => 'select',
                            'class'                      => '',
                            'source'                     => 'eav/entity_attribute_source_boolean',
                            'global'                     => Mage_Catalog_Model_Resource_Eav_Attribute::SCOPE_WEBSITE,
                            'visible'                    => true,
                            'required'                   => false,
                            'user_defined'               => true,
                            'default'                    => false,
                            'searchable'                 => true,
                            'filterable'                 => true,
                            'comparable'                 => false,
                            'visible_on_front'           => true,
                            'visible_in_advanced_search' => true,
                            'used_in_product_listing'    => true,
                            'used_for_sort_by'           => true,
                            'unique'                     => false,
                            'apply_to'                   => 'configurable,simple',
                        ),
                    ),
                ),
            );
    }
}

I see you've found a solution to your problem, but I thought it worth to add a note:

Since Magento 1.7 you should use Mage_Catalog_Model_Resource_Setup instead of Mage_Eav_Model_Entity_Setup and it will deal with the apply_to setting and many others:

protected function _prepareValues($attr)
{
    $data = parent::_prepareValues($attr);
    $data = array_merge($data, array(
        'frontend_input_renderer'       => $this->_getValue($attr, 'input_renderer'),
        'is_global'                     => $this->_getValue(
            $attr,
            'global',
            Mage_Catalog_Model_Resource_Eav_Attribute::SCOPE_GLOBAL
        ),
        'is_visible'                    => $this->_getValue($attr, 'visible', 1),
        'is_searchable'                 => $this->_getValue($attr, 'searchable', 0),
        'is_filterable'                 => $this->_getValue($attr, 'filterable', 0),
        'is_comparable'                 => $this->_getValue($attr, 'comparable', 0),
        'is_visible_on_front'           => $this->_getValue($attr, 'visible_on_front', 0),
        'is_wysiwyg_enabled'            => $this->_getValue($attr, 'wysiwyg_enabled', 0),
        'is_html_allowed_on_front'      => $this->_getValue($attr, 'is_html_allowed_on_front', 0),
        'is_visible_in_advanced_search' => $this->_getValue($attr, 'visible_in_advanced_search', 0),
        'is_filterable_in_search'       => $this->_getValue($attr, 'filterable_in_search', 0),
        'used_in_product_listing'       => $this->_getValue($attr, 'used_in_product_listing', 0),
        'used_for_sort_by'              => $this->_getValue($attr, 'used_for_sort_by', 0),
        'apply_to'                      => $this->_getValue($attr, 'apply_to'),
        'position'                      => $this->_getValue($attr, 'position', 0),
        'is_configurable'               => $this->_getValue($attr, 'is_configurable', 1),
        'is_used_for_promo_rules'       => $this->_getValue($attr, 'used_for_promo_rules', 0)
    ));
    return $data;
}

The attribute you are looking for is apply_to, e.g.

'apply_to' => array('configurable'),